------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:34:27 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.32 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.32 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6590E+04 1.7254E+01 1.3176E+02 C 23783 BOND = 8432.9836 ANGLE = 22191.6806 DIHED = 32413.6116 VDWAALS = -24252.4552 EEL = -190990.4100 EGB = -62565.4668 1-4 VDW = 10750.5433 1-4 EEL = 146458.4934 RESTRAINT = 0.0000 ESURF = 971.1130 minimization completed, ENE= -.56589907E+05 RMS= 0.172543E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6638E+04 1.7288E+01 1.4114E+02 C 36759 BOND = 8356.0260 ANGLE = 22326.9740 DIHED = 32461.6793 VDWAALS = -24395.4165 EEL = -190447.8308 EGB = -62723.6431 1-4 VDW = 10688.1435 1-4 EEL = 146122.4569 RESTRAINT = 0.0000 ESURF = 973.5370 minimization completed, ENE= -.56638074E+05 RMS= 0.172875E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6539E+04 1.7314E+01 1.2120E+02 CB 18353 BOND = 8351.1912 ANGLE = 22331.1553 DIHED = 32430.5290 VDWAALS = -24293.8468 EEL = -189960.9863 EGB = -63167.1498 1-4 VDW = 10679.9521 1-4 EEL = 146111.8083 RESTRAINT = 0.0000 ESURF = 977.8578 minimization completed, ENE= -.56539489E+05 RMS= 0.173141E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6583E+04 1.7326E+01 1.3110E+02 C 33218 BOND = 8318.2245 ANGLE = 22290.3505 DIHED = 32293.4343 VDWAALS = -24160.9123 EEL = -190305.1783 EGB = -63003.5946 1-4 VDW = 10750.8548 1-4 EEL = 146258.6677 RESTRAINT = 0.0000 ESURF = 975.5819 minimization completed, ENE= -.56582572E+05 RMS= 0.173264E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6796E+04 1.7307E+01 1.3689E+02 C 28805 BOND = 8403.3333 ANGLE = 22134.6877 DIHED = 32290.4894 VDWAALS = -24238.3363 EEL = -190865.7719 EGB = -62407.9793 1-4 VDW = 10747.0105 1-4 EEL = 146166.1950 RESTRAINT = 0.0000 ESURF = 974.1694 minimization completed, ENE= -.56796202E+05 RMS= 0.173072E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6716E+04 1.7276E+01 1.4337E+02 C 46319 BOND = 8281.5359 ANGLE = 22504.9390 DIHED = 32251.5534 VDWAALS = -24231.1577 EEL = -190603.5910 EGB = -62850.8222 1-4 VDW = 10702.2037 1-4 EEL = 146250.1155 RESTRAINT = 0.0000 ESURF = 979.0101 minimization completed, ENE= -.56716213E+05 RMS= 0.172765E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6823E+04 1.7317E+01 1.3435E+02 C 42929 BOND = 8360.8229 ANGLE = 22164.2584 DIHED = 32314.7185 VDWAALS = -24300.1573 EEL = -190940.4732 EGB = -62350.6844 1-4 VDW = 10740.2574 1-4 EEL = 146216.6314 RESTRAINT = 0.0000 ESURF = 971.9302 minimization completed, ENE= -.56822696E+05 RMS= 0.173168E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6257E+04 1.7389E+01 1.3860E+02 C 15085 BOND = 8409.3329 ANGLE = 22439.3239 DIHED = 32434.1403 VDWAALS = -24099.6510 EEL = -190969.0999 EGB = -62496.6101 1-4 VDW = 10716.2009 1-4 EEL = 146329.8714 RESTRAINT = 0.0000 ESURF = 979.0967 minimization completed, ENE= -.56257395E+05 RMS= 0.173889E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6456E+04 1.7305E+01 1.1836E+02 CG 26237 BOND = 8414.0340 ANGLE = 22189.9355 DIHED = 32463.4558 VDWAALS = -24132.0600 EEL = -190820.7741 EGB = -62489.1528 1-4 VDW = 10727.8987 1-4 EEL = 146216.2767 RESTRAINT = 0.0000 ESURF = 973.9177 minimization completed, ENE= -.56456468E+05 RMS= 0.173053E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6172E+04 1.7399E+01 1.5419E+02 C 43640 BOND = 8445.3336 ANGLE = 22589.1913 DIHED = 32476.6859 VDWAALS = -24177.2866 EEL = -191112.8021 EGB = -62449.1008 1-4 VDW = 10721.5752 1-4 EEL = 146354.8491 RESTRAINT = 0.0000 ESURF = 979.5496 minimization completed, ENE= -.56172005E+05 RMS= 0.173985E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6350E+04 1.7465E+01 1.2916E+02 N 23297 BOND = 8458.2635 ANGLE = 22366.4466 DIHED = 32476.8355 VDWAALS = -24221.3958 EEL = -190701.0687 EGB = -62559.0863 1-4 VDW = 10672.0475 1-4 EEL = 146181.5920 RESTRAINT = 0.0000 ESURF = 976.6902 minimization completed, ENE= -.56349675E+05 RMS= 0.174653E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6681E+04 1.7359E+01 1.4536E+02 N 26479 BOND = 8483.4319 ANGLE = 22101.5741 DIHED = 32322.6961 VDWAALS = -24207.0346 EEL = -190578.9042 EGB = -62685.7401 1-4 VDW = 10703.3680 1-4 EEL = 146200.1636 RESTRAINT = 0.0000 ESURF = 979.4501 minimization completed, ENE= -.56680995E+05 RMS= 0.173587E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6590E+04 1.7414E+01 1.6142E+02 C 41712 BOND = 8521.1669 ANGLE = 22273.3313 DIHED = 32417.7476 VDWAALS = -24171.8281 EEL = -190604.5154 EGB = -62870.8198 1-4 VDW = 10764.0088 1-4 EEL = 146097.1254 RESTRAINT = 0.0000 ESURF = 983.7056 minimization completed, ENE= -.56590078E+05 RMS= 0.174141E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6468E+04 1.7315E+01 1.3800E+02 C 29582 BOND = 8330.3950 ANGLE = 22308.1437 DIHED = 32470.1328 VDWAALS = -24241.8789 EEL = -190698.6296 EGB = -62782.3741 1-4 VDW = 10741.8196 1-4 EEL = 146426.0958 RESTRAINT = 0.0000 ESURF = 977.9046 minimization completed, ENE= -.56468391E+05 RMS= 0.173152E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6569E+04 1.7301E+01 1.3212E+02 C 37468 BOND = 8253.8181 ANGLE = 22258.2230 DIHED = 32493.0069 VDWAALS = -24048.4755 EEL = -190348.8414 EGB = -63141.3785 1-4 VDW = 10732.1516 1-4 EEL = 146249.3863 RESTRAINT = 0.0000 ESURF = 982.8990 minimization completed, ENE= -.56569210E+05 RMS= 0.173011E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6387E+04 1.7382E+01 1.4035E+02 C 6725 BOND = 8529.5702 ANGLE = 22477.2664 DIHED = 32446.0698 VDWAALS = -24265.8153 EEL = -189907.7572 EGB = -63205.8571 1-4 VDW = 10577.2927 1-4 EEL = 145977.8938 RESTRAINT = 0.0000 ESURF = 983.9821 minimization completed, ENE= -.56387355E+05 RMS= 0.173819E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6635E+04 1.7264E+01 1.2668E+02 C 40436 BOND = 8301.1628 ANGLE = 22257.0343 DIHED = 32550.6111 VDWAALS = -24273.2279 EEL = -190686.1185 EGB = -62666.4127 1-4 VDW = 10734.0891 1-4 EEL = 146166.4170 RESTRAINT = 0.0000 ESURF = 981.8945 minimization completed, ENE= -.56634550E+05 RMS= 0.172642E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6693E+04 1.7283E+01 1.2005E+02 CG 39227 BOND = 8326.1029 ANGLE = 22221.9380 DIHED = 32419.6472 VDWAALS = -24133.1193 EEL = -191318.2657 EGB = -62261.0869 1-4 VDW = 10772.2992 1-4 EEL = 146296.4069 RESTRAINT = 0.0000 ESURF = 983.4587 minimization completed, ENE= -.56692619E+05 RMS= 0.172830E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6852E+04 1.7302E+01 1.2884E+02 C 11377 BOND = 8253.7857 ANGLE = 22127.0010 DIHED = 32382.5089 VDWAALS = -24171.6295 EEL = -190571.2204 EGB = -62945.8196 1-4 VDW = 10749.6545 1-4 EEL = 146335.8521 RESTRAINT = 0.0000 ESURF = 988.0705 minimization completed, ENE= -.56851797E+05 RMS= 0.173024E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6576E+04 1.7298E+01 1.2201E+02 CG 38599 BOND = 8373.1346 ANGLE = 22182.4613 DIHED = 32419.9397 VDWAALS = -24203.9707 EEL = -190406.4203 EGB = -62847.4278 1-4 VDW = 10820.2556 1-4 EEL = 146098.1034 RESTRAINT = 0.0000 ESURF = 988.2156 minimization completed, ENE= -.56575709E+05 RMS= 0.172983E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6586E+04 1.7376E+01 1.3047E+02 C 14653 BOND = 8412.5567 ANGLE = 22241.9393 DIHED = 32484.8335 VDWAALS = -24194.8977 EEL = -190701.8868 EGB = -62785.5742 1-4 VDW = 10745.3605 1-4 EEL = 146227.1480 RESTRAINT = 0.0000 ESURF = 984.0507 minimization completed, ENE= -.56586470E+05 RMS= 0.173764E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6596E+04 1.7253E+01 1.3490E+02 CD 28689 BOND = 8337.5480 ANGLE = 22289.4747 DIHED = 32429.9290 VDWAALS = -24070.9747 EEL = -190159.4900 EGB = -63261.7233 1-4 VDW = 10771.6986 1-4 EEL = 146077.8997 RESTRAINT = 0.0000 ESURF = 989.3403 minimization completed, ENE= -.56596298E+05 RMS= 0.172532E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6853E+04 1.7328E+01 1.2260E+02 C 43549 BOND = 8339.3108 ANGLE = 22277.6516 DIHED = 32394.5421 VDWAALS = -24165.2231 EEL = -190925.1959 EGB = -62902.8573 1-4 VDW = 10732.3890 1-4 EEL = 146407.2859 RESTRAINT = 0.0000 ESURF = 988.8419 minimization completed, ENE= -.56853255E+05 RMS= 0.173285E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6580E+04 1.7296E+01 1.2500E+02 N 16054 BOND = 8351.5272 ANGLE = 22375.9790 DIHED = 32299.1496 VDWAALS = -24120.0883 EEL = -190885.0885 EGB = -62685.9228 1-4 VDW = 10762.1866 1-4 EEL = 146333.9546 RESTRAINT = 0.0000 ESURF = 988.7806 minimization completed, ENE= -.56579522E+05 RMS= 0.172957E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6713E+04 1.7168E+01 1.2840E+02 N 23162 BOND = 8192.5928 ANGLE = 22307.4363 DIHED = 32403.8338 VDWAALS = -24253.5222 EEL = -190557.2594 EGB = -62958.5794 1-4 VDW = 10758.7826 1-4 EEL = 146408.9921 RESTRAINT = 0.0000 ESURF = 985.1904 minimization completed, ENE= -.56712533E+05 RMS= 0.171685E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2886.36 ( 5.02% of Gen B) | Calc gb diag 13798.95 (23.99% of Gen B) | Calc gb off-diag 40841.57 (71.00% of Gen B) | Gen Born time 57526.88 (100.0% of Nonbo) | Nonbond force 57526.88 (100.0% of Force) | Bond/Angle/Dihedral 17.33 ( 0.03% of Force) | Force time 57544.24 (100.0% of Runmd) | Runmd Time 57544.24 (99.85% of Total) | Other 88.56 ( 0.15% of Total) | Total time 57632.93 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:34:27.033 on 10/17/2010 | Setup done at 07:34:29.541 on 10/17/2010 | Run done at 23:34:59.960 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:34:19 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.31 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.31 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6394E+04 1.7380E+01 1.2990E+02 C 1349 BOND = 8442.1477 ANGLE = 22363.7248 DIHED = 32509.1089 VDWAALS = -24080.3511 EEL = -190916.7170 EGB = -62477.7146 1-4 VDW = 10715.0309 1-4 EEL = 146068.8816 RESTRAINT = 0.0000 ESURF = 982.0542 minimization completed, ENE= -.56393835E+05 RMS= 0.173795E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6554E+04 1.7361E+01 1.1983E+02 C 44706 BOND = 8449.7937 ANGLE = 22283.1057 DIHED = 32463.7085 VDWAALS = -24123.6089 EEL = -190670.6018 EGB = -62757.4389 1-4 VDW = 10729.1350 1-4 EEL = 146088.9758 RESTRAINT = 0.0000 ESURF = 982.6556 minimization completed, ENE= -.56554276E+05 RMS= 0.173613E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6330E+04 1.7361E+01 1.2928E+02 C 34365 BOND = 8401.3137 ANGLE = 22353.8118 DIHED = 32455.4172 VDWAALS = -24172.9771 EEL = -190764.1372 EGB = -62505.0795 1-4 VDW = 10778.1422 1-4 EEL = 146142.7897 RESTRAINT = 0.0000 ESURF = 981.1427 minimization completed, ENE= -.56329576E+05 RMS= 0.173606E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6592E+04 1.7354E+01 1.3796E+02 CZ 15941 BOND = 8334.3077 ANGLE = 22251.7772 DIHED = 32369.7644 VDWAALS = -24060.8168 EEL = -190631.8436 EGB = -62798.1003 1-4 VDW = 10841.0648 1-4 EEL = 146115.5617 RESTRAINT = 0.0000 ESURF = 985.7945 minimization completed, ENE= -.56592490E+05 RMS= 0.173539E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6397E+04 1.7349E+01 1.1807E+02 C 17629 BOND = 8416.7287 ANGLE = 22371.7324 DIHED = 32497.0868 VDWAALS = -24167.3695 EEL = -190707.2681 EGB = -62767.6935 1-4 VDW = 10733.6518 1-4 EEL = 146243.3357 RESTRAINT = 0.0000 ESURF = 982.9858 minimization completed, ENE= -.56396810E+05 RMS= 0.173488E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6313E+04 1.7383E+01 1.2244E+02 C 40924 BOND = 8312.5657 ANGLE = 22389.4093 DIHED = 32469.1946 VDWAALS = -24154.1510 EEL = -190867.7155 EGB = -62415.2285 1-4 VDW = 10846.1648 1-4 EEL = 146129.1964 RESTRAINT = 0.0000 ESURF = 977.2718 minimization completed, ENE= -.56313292E+05 RMS= 0.173833E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6218E+04 1.7445E+01 1.2533E+02 C 37532 BOND = 8461.0444 ANGLE = 22388.1673 DIHED = 32559.1239 VDWAALS = -24135.5796 EEL = -190877.9932 EGB = -62522.4291 1-4 VDW = 10754.6601 1-4 EEL = 146172.9832 RESTRAINT = 0.0000 ESURF = 982.1037 minimization completed, ENE= -.56217919E+05 RMS= 0.174447E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6260E+04 1.7425E+01 1.2742E+02 C 10495 BOND = 8395.2144 ANGLE = 22551.1266 DIHED = 32365.3733 VDWAALS = -24216.5374 EEL = -190576.8140 EGB = -62609.4596 1-4 VDW = 10680.4871 1-4 EEL = 146162.4655 RESTRAINT = 0.0000 ESURF = 988.5090 minimization completed, ENE= -.56259635E+05 RMS= 0.174249E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6693E+04 1.7280E+01 1.2203E+02 C 2403 BOND = 8374.0022 ANGLE = 22162.3913 DIHED = 32337.1651 VDWAALS = -24187.9939 EEL = -190478.4496 EGB = -62850.0782 1-4 VDW = 10744.4246 1-4 EEL = 146222.7234 RESTRAINT = 0.0000 ESURF = 982.6383 minimization completed, ENE= -.56693177E+05 RMS= 0.172804E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6539E+04 1.7295E+01 1.3255E+02 C 12619 BOND = 8353.2411 ANGLE = 22314.6037 DIHED = 32433.3283 VDWAALS = -24183.2991 EEL = -190109.4222 EGB = -63000.2999 1-4 VDW = 10718.5005 1-4 EEL = 145956.1340 RESTRAINT = 0.0000 ESURF = 978.6458 minimization completed, ENE= -.56538568E+05 RMS= 0.172950E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6453E+04 1.7436E+01 1.2320E+02 NE2 13098 BOND = 8422.3708 ANGLE = 22373.3678 DIHED = 32482.7932 VDWAALS = -24151.1465 EEL = -190744.7817 EGB = -62812.6907 1-4 VDW = 10722.9934 1-4 EEL = 146273.9769 RESTRAINT = 0.0000 ESURF = 980.1691 minimization completed, ENE= -.56452948E+05 RMS= 0.174362E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6727E+04 1.7340E+01 1.2695E+02 C 28603 BOND = 8454.2598 ANGLE = 22371.7885 DIHED = 32347.8066 VDWAALS = -24279.6034 EEL = -190598.1387 EGB = -62785.1596 1-4 VDW = 10680.5545 1-4 EEL = 146098.0257 RESTRAINT = 0.0000 ESURF = 983.0558 minimization completed, ENE= -.56727411E+05 RMS= 0.173401E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6609E+04 1.7289E+01 1.1365E+02 C 113 BOND = 8342.9151 ANGLE = 22321.8405 DIHED = 32441.7641 VDWAALS = -24105.3916 EEL = -190640.1705 EGB = -62726.7240 1-4 VDW = 10718.0725 1-4 EEL = 146062.2371 RESTRAINT = 0.0000 ESURF = 976.4056 minimization completed, ENE= -.56609051E+05 RMS= 0.172893E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6667E+04 1.7228E+01 1.3090E+02 C 5362 BOND = 8387.4015 ANGLE = 22237.9737 DIHED = 32417.2440 VDWAALS = -24153.1881 EEL = -190846.6830 EGB = -62701.9855 1-4 VDW = 10698.4441 1-4 EEL = 146320.4671 RESTRAINT = 0.0000 ESURF = 973.5735 minimization completed, ENE= -.56666753E+05 RMS= 0.172283E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6473E+04 1.7356E+01 1.7375E+02 C 8378 BOND = 8312.6944 ANGLE = 22483.3122 DIHED = 32387.7751 VDWAALS = -24110.5377 EEL = -190983.0966 EGB = -62740.1231 1-4 VDW = 10755.8562 1-4 EEL = 146441.8932 RESTRAINT = 0.0000 ESURF = 978.9178 minimization completed, ENE= -.56473308E+05 RMS= 0.173561E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6572E+04 1.7320E+01 1.2071E+02 CD 30026 BOND = 8419.8978 ANGLE = 22218.1514 DIHED = 32386.2675 VDWAALS = -24186.1975 EEL = -190275.7601 EGB = -63138.0002 1-4 VDW = 10751.8477 1-4 EEL = 146268.5498 RESTRAINT = 0.0000 ESURF = 983.4336 minimization completed, ENE= -.56571810E+05 RMS= 0.173196E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6437E+04 1.7392E+01 1.2247E+02 CG 25758 BOND = 8529.5910 ANGLE = 22265.0335 DIHED = 32509.2137 VDWAALS = -24179.4884 EEL = -190522.7236 EGB = -63095.2295 1-4 VDW = 10729.7718 1-4 EEL = 146350.6354 RESTRAINT = 0.0000 ESURF = 976.0156 minimization completed, ENE= -.56437180E+05 RMS= 0.173916E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6696E+04 1.7226E+01 1.3089E+02 C 23248 BOND = 8221.0688 ANGLE = 22204.6193 DIHED = 32407.7661 VDWAALS = -24219.9620 EEL = -190595.1782 EGB = -62802.9933 1-4 VDW = 10808.6025 1-4 EEL = 146304.7803 RESTRAINT = 0.0000 ESURF = 975.6000 minimization completed, ENE= -.56695697E+05 RMS= 0.172257E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6580E+04 1.7271E+01 1.2058E+02 N 39830 BOND = 8390.7668 ANGLE = 22283.3999 DIHED = 32515.7816 VDWAALS = -24204.0141 EEL = -190462.8437 EGB = -62963.8796 1-4 VDW = 10678.5689 1-4 EEL = 146203.5320 RESTRAINT = 0.0000 ESURF = 978.3997 minimization completed, ENE= -.56580288E+05 RMS= 0.172708E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6947E+04 1.7245E+01 1.3258E+02 C 40648 BOND = 8269.6731 ANGLE = 22183.7344 DIHED = 32339.8158 VDWAALS = -24305.0744 EEL = -190742.5203 EGB = -62851.0931 1-4 VDW = 10730.6580 1-4 EEL = 146454.6951 RESTRAINT = 0.0000 ESURF = 972.8071 minimization completed, ENE= -.56947304E+05 RMS= 0.172454E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6838E+04 1.7293E+01 1.1792E+02 C 40210 BOND = 8381.6234 ANGLE = 22074.7621 DIHED = 32464.9361 VDWAALS = -24331.7993 EEL = -190654.1748 EGB = -62548.5551 1-4 VDW = 10663.9816 1-4 EEL = 146142.2975 RESTRAINT = 0.0000 ESURF = 969.3652 minimization completed, ENE= -.56837563E+05 RMS= 0.172927E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6637E+04 1.7313E+01 1.4925E+02 C 17198 BOND = 8474.4066 ANGLE = 22242.6378 DIHED = 32442.6616 VDWAALS = -24264.4155 EEL = -190797.7777 EGB = -62672.2908 1-4 VDW = 10678.5579 1-4 EEL = 146287.8524 RESTRAINT = 0.0000 ESURF = 971.5356 minimization completed, ENE= -.56636832E+05 RMS= 0.173126E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6628E+04 1.7361E+01 1.3790E+02 C 33794 BOND = 8440.1775 ANGLE = 22114.5621 DIHED = 32455.4072 VDWAALS = -24192.8057 EEL = -190762.5514 EGB = -62621.2390 1-4 VDW = 10757.1270 1-4 EEL = 146204.1854 RESTRAINT = 0.0000 ESURF = 976.8755 minimization completed, ENE= -.56628261E+05 RMS= 0.173606E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6600E+04 1.7393E+01 1.3807E+02 CB 2562 BOND = 8406.4411 ANGLE = 22367.7585 DIHED = 32352.4871 VDWAALS = -24226.4255 EEL = -190515.1155 EGB = -62764.7418 1-4 VDW = 10699.9750 1-4 EEL = 146102.3716 RESTRAINT = 0.0000 ESURF = 977.7304 minimization completed, ENE= -.56599519E+05 RMS= 0.173935E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6670E+04 1.7320E+01 1.2745E+02 C 17450 BOND = 8411.4548 ANGLE = 22129.1430 DIHED = 32429.7605 VDWAALS = -24323.9321 EEL = -190200.7749 EGB = -63166.2545 1-4 VDW = 10770.2762 1-4 EEL = 146312.1788 RESTRAINT = 0.0000 ESURF = 968.6250 minimization completed, ENE= -.56669523E+05 RMS= 0.173195E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2878.41 ( 5.01% of Gen B) | Calc gb diag 13883.10 (24.16% of Gen B) | Calc gb off-diag 40691.88 (70.83% of Gen B) | Gen Born time 57453.41 (100.0% of Nonbo) | Nonbond force 57453.41 (100.0% of Force) | Bond/Angle/Dihedral 16.99 ( 0.03% of Force) | Force time 57470.43 (100.0% of Runmd) | Runmd Time 57470.43 (99.85% of Total) | Other 87.31 ( 0.15% of Total) | Total time 57558.06 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:34:19.767 on 10/17/2010 | Setup done at 07:34:21.957 on 10/17/2010 | Run done at 23:33:37.826 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:34:14 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.30 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.30 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6377E+04 1.7387E+01 1.1908E+02 CZ 36864 BOND = 8455.2734 ANGLE = 22202.7489 DIHED = 32405.9122 VDWAALS = -24134.6846 EEL = -190550.5756 EGB = -62824.2888 1-4 VDW = 10795.6390 1-4 EEL = 146286.1478 RESTRAINT = 0.0000 ESURF = 986.7711 minimization completed, ENE= -.56377057E+05 RMS= 0.173873E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6483E+04 1.7380E+01 1.2781E+02 C 26964 BOND = 8353.2247 ANGLE = 22294.0831 DIHED = 32387.4672 VDWAALS = -24060.7562 EEL = -190528.1068 EGB = -62929.5056 1-4 VDW = 10753.0906 1-4 EEL = 146259.3615 RESTRAINT = 0.0000 ESURF = 987.9997 minimization completed, ENE= -.56483142E+05 RMS= 0.173798E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6603E+04 1.7226E+01 1.4327E+02 C 26552 BOND = 8350.7456 ANGLE = 22255.7075 DIHED = 32386.1188 VDWAALS = -24085.9295 EEL = -190532.5641 EGB = -62925.9369 1-4 VDW = 10722.0756 1-4 EEL = 146241.0919 RESTRAINT = 0.0000 ESURF = 986.0536 minimization completed, ENE= -.56602638E+05 RMS= 0.172260E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6409E+04 1.7333E+01 1.1846E+02 CG 45573 BOND = 8388.2634 ANGLE = 22251.8684 DIHED = 32466.6909 VDWAALS = -24080.1739 EEL = -190489.1684 EGB = -62946.8165 1-4 VDW = 10782.8319 1-4 EEL = 146228.8379 RESTRAINT = 0.0000 ESURF = 988.5519 minimization completed, ENE= -.56409115E+05 RMS= 0.173327E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6596E+04 1.7353E+01 1.2229E+02 C 28454 BOND = 8436.6953 ANGLE = 22244.5898 DIHED = 32387.6732 VDWAALS = -24083.1372 EEL = -190907.5264 EGB = -62678.9307 1-4 VDW = 10753.0640 1-4 EEL = 146265.9392 RESTRAINT = 0.0000 ESURF = 985.3450 minimization completed, ENE= -.56596288E+05 RMS= 0.173532E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6485E+04 1.7367E+01 1.3720E+02 CD2 24176 BOND = 8381.1993 ANGLE = 22488.4431 DIHED = 32444.7911 VDWAALS = -24109.3435 EEL = -190848.7758 EGB = -62632.8066 1-4 VDW = 10718.1534 1-4 EEL = 146087.8359 RESTRAINT = 0.0000 ESURF = 985.1642 minimization completed, ENE= -.56485339E+05 RMS= 0.173668E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6738E+04 1.7244E+01 1.3367E+02 C 25357 BOND = 8304.6649 ANGLE = 22227.0853 DIHED = 32366.1931 VDWAALS = -24029.9675 EEL = -191226.6115 EGB = -62194.4284 1-4 VDW = 10765.1603 1-4 EEL = 146064.4088 RESTRAINT = 0.0000 ESURF = 985.8453 minimization completed, ENE= -.56737650E+05 RMS= 0.172439E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6597E+04 1.7281E+01 1.5219E+02 C 41629 BOND = 8309.8533 ANGLE = 22435.2892 DIHED = 32395.2264 VDWAALS = -24173.7501 EEL = -191308.1588 EGB = -62175.9199 1-4 VDW = 10701.7362 1-4 EEL = 146236.1212 RESTRAINT = 0.0000 ESURF = 982.9117 minimization completed, ENE= -.56596691E+05 RMS= 0.172811E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6621E+04 1.7309E+01 1.4103E+02 CD 9740 BOND = 8408.2109 ANGLE = 22263.0050 DIHED = 32376.3784 VDWAALS = -24284.3955 EEL = -190865.1166 EGB = -62559.8129 1-4 VDW = 10777.5281 1-4 EEL = 146282.2735 RESTRAINT = 0.0000 ESURF = 981.0192 minimization completed, ENE= -.56620910E+05 RMS= 0.173088E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6696E+04 1.7325E+01 1.3294E+02 CG 9069 BOND = 8528.1351 ANGLE = 22259.0401 DIHED = 32347.9577 VDWAALS = -24218.5606 EEL = -191018.8396 EGB = -62383.1534 1-4 VDW = 10728.2791 1-4 EEL = 146077.4400 RESTRAINT = 0.0000 ESURF = 983.7037 minimization completed, ENE= -.56695998E+05 RMS= 0.173247E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6765E+04 1.7359E+01 1.4513E+02 C 26760 BOND = 8353.3000 ANGLE = 22288.5414 DIHED = 32396.0594 VDWAALS = -24141.4369 EEL = -191093.6789 EGB = -62452.4325 1-4 VDW = 10723.4107 1-4 EEL = 146177.6170 RESTRAINT = 0.0000 ESURF = 983.7665 minimization completed, ENE= -.56764853E+05 RMS= 0.173591E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6696E+04 1.7292E+01 1.2528E+02 C 39186 BOND = 8375.1746 ANGLE = 22161.3858 DIHED = 32369.7141 VDWAALS = -24072.0964 EEL = -190758.6692 EGB = -62687.4771 1-4 VDW = 10734.2645 1-4 EEL = 146196.1957 RESTRAINT = 0.0000 ESURF = 985.6485 minimization completed, ENE= -.56695860E+05 RMS= 0.172922E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6810E+04 1.7320E+01 1.2395E+02 CG 26357 BOND = 8327.9676 ANGLE = 22260.3808 DIHED = 32396.2698 VDWAALS = -24123.9973 EEL = -190884.8386 EGB = -62674.2613 1-4 VDW = 10699.9240 1-4 EEL = 146199.7965 RESTRAINT = 0.0000 ESURF = 988.7967 minimization completed, ENE= -.56809962E+05 RMS= 0.173197E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6833E+04 1.7319E+01 1.3458E+02 CD 38559 BOND = 8354.9482 ANGLE = 22239.3280 DIHED = 32331.2012 VDWAALS = -24078.6206 EEL = -191373.1316 EGB = -62088.4632 1-4 VDW = 10684.1506 1-4 EEL = 146115.8516 RESTRAINT = 0.0000 ESURF = 981.4302 minimization completed, ENE= -.56833305E+05 RMS= 0.173188E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6654E+04 1.7369E+01 1.4400E+02 C 30304 BOND = 8556.8141 ANGLE = 22284.3602 DIHED = 32371.0039 VDWAALS = -24231.8283 EEL = -190547.6892 EGB = -62681.1353 1-4 VDW = 10657.3569 1-4 EEL = 145951.3472 RESTRAINT = 0.0000 ESURF = 985.3324 minimization completed, ENE= -.56654438E+05 RMS= 0.173692E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6685E+04 1.7375E+01 1.4511E+02 CD 35862 BOND = 8366.6082 ANGLE = 22282.8079 DIHED = 32427.8356 VDWAALS = -24114.1495 EEL = -191002.6429 EGB = -62448.0563 1-4 VDW = 10750.9505 1-4 EEL = 146064.0980 RESTRAINT = 0.0000 ESURF = 987.2170 minimization completed, ENE= -.56685331E+05 RMS= 0.173753E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6936E+04 1.7233E+01 1.2963E+02 C 13230 BOND = 8347.8347 ANGLE = 22214.0382 DIHED = 32375.2919 VDWAALS = -24088.1522 EEL = -191787.5833 EGB = -61906.5777 1-4 VDW = 10716.2779 1-4 EEL = 146206.8264 RESTRAINT = 0.0000 ESURF = 985.8218 minimization completed, ENE= -.56936222E+05 RMS= 0.172331E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6447E+04 1.7469E+01 1.3664E+02 C 1550 BOND = 8387.6634 ANGLE = 22350.7295 DIHED = 32409.5709 VDWAALS = -24136.0941 EEL = -190818.6402 EGB = -62806.4134 1-4 VDW = 10793.3044 1-4 EEL = 146388.4680 RESTRAINT = 0.0000 ESURF = 984.6148 minimization completed, ENE= -.56446797E+05 RMS= 0.174693E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6540E+04 1.7318E+01 1.2691E+02 C 29352 BOND = 8347.1326 ANGLE = 22332.1782 DIHED = 32399.1467 VDWAALS = -24070.6753 EEL = -190710.5575 EGB = -62654.8369 1-4 VDW = 10766.7341 1-4 EEL = 146068.2932 RESTRAINT = 0.0000 ESURF = 982.4052 minimization completed, ENE= -.56540180E+05 RMS= 0.173185E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6320E+04 1.7409E+01 1.3929E+02 CG 30011 BOND = 8402.2860 ANGLE = 22573.1312 DIHED = 32438.7845 VDWAALS = -24140.3031 EEL = -190882.8934 EGB = -62463.0717 1-4 VDW = 10697.7660 1-4 EEL = 146074.5941 RESTRAINT = 0.0000 ESURF = 979.7891 minimization completed, ENE= -.56319917E+05 RMS= 0.174092E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6648E+04 1.7296E+01 1.1696E+02 CD 12357 BOND = 8400.6312 ANGLE = 22358.5427 DIHED = 32294.5093 VDWAALS = -24147.7039 EEL = -190943.4629 EGB = -62564.7711 1-4 VDW = 10744.7434 1-4 EEL = 146223.6653 RESTRAINT = 0.0000 ESURF = 986.1734 minimization completed, ENE= -.56647673E+05 RMS= 0.172963E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6611E+04 1.7227E+01 1.3166E+02 C 30188 BOND = 8294.8586 ANGLE = 22329.2663 DIHED = 32384.0239 VDWAALS = -24255.2377 EEL = -190368.8519 EGB = -62879.9823 1-4 VDW = 10753.1608 1-4 EEL = 146153.3828 RESTRAINT = 0.0000 ESURF = 978.4488 minimization completed, ENE= -.56610931E+05 RMS= 0.172275E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6669E+04 1.7253E+01 1.2391E+02 C 41645 BOND = 8339.8180 ANGLE = 22291.5693 DIHED = 32405.8250 VDWAALS = -24207.3056 EEL = -190460.6271 EGB = -62983.8694 1-4 VDW = 10704.4629 1-4 EEL = 146256.4666 RESTRAINT = 0.0000 ESURF = 984.7859 minimization completed, ENE= -.56668874E+05 RMS= 0.172528E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6499E+04 1.7337E+01 1.2675E+02 C 39764 BOND = 8434.9862 ANGLE = 22414.9454 DIHED = 32466.7860 VDWAALS = -24168.6194 EEL = -190843.9896 EGB = -62817.1946 1-4 VDW = 10719.5730 1-4 EEL = 146308.3072 RESTRAINT = 0.0000 ESURF = 986.2294 minimization completed, ENE= -.56498976E+05 RMS= 0.173366E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6747E+04 1.7366E+01 1.2056E+02 C 8904 BOND = 8432.8537 ANGLE = 22085.3859 DIHED = 32379.4869 VDWAALS = -24152.0288 EEL = -190912.6593 EGB = -62615.8959 1-4 VDW = 10754.6920 1-4 EEL = 146291.3602 RESTRAINT = 0.0000 ESURF = 990.2806 minimization completed, ENE= -.56746525E+05 RMS= 0.173658E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2862.69 ( 4.98% of Gen B) | Calc gb diag 13869.97 (24.15% of Gen B) | Calc gb off-diag 40703.60 (70.87% of Gen B) | Gen Born time 57436.28 (100.0% of Nonbo) | Nonbond force 57436.28 (100.0% of Force) | Bond/Angle/Dihedral 17.59 ( 0.03% of Force) | Force time 57453.89 (100.0% of Runmd) | Runmd Time 57453.89 (99.85% of Total) | Other 85.68 ( 0.15% of Total) | Total time 57539.71 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:34:14.125 on 10/17/2010 | Setup done at 07:34:16.790 on 10/17/2010 | Run done at 23:33:13.833 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:34:07 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.29 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.29 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6643E+04 1.7379E+01 1.4084E+02 CG 16957 BOND = 8598.1218 ANGLE = 22187.6164 DIHED = 32370.6265 VDWAALS = -24210.4524 EEL = -190960.3449 EGB = -62359.7462 1-4 VDW = 10665.3748 1-4 EEL = 146078.1500 RESTRAINT = 0.0000 ESURF = 987.4205 minimization completed, ENE= -.56643234E+05 RMS= 0.173785E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6355E+04 1.7419E+01 1.3043E+02 CZ 11255 BOND = 8369.3775 ANGLE = 22511.3482 DIHED = 32394.3257 VDWAALS = -24106.7790 EEL = -190919.2124 EGB = -62428.4060 1-4 VDW = 10686.7985 1-4 EEL = 146153.0937 RESTRAINT = 0.0000 ESURF = 984.7727 minimization completed, ENE= -.56354681E+05 RMS= 0.174187E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6524E+04 1.7318E+01 1.2976E+02 N 19056 BOND = 8448.9621 ANGLE = 22213.8935 DIHED = 32459.8676 VDWAALS = -24011.0554 EEL = -191248.3274 EGB = -62404.1127 1-4 VDW = 10740.0054 1-4 EEL = 146289.5100 RESTRAINT = 0.0000 ESURF = 987.7361 minimization completed, ENE= -.56523521E+05 RMS= 0.173184E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6541E+04 1.7384E+01 1.3010E+02 C 20692 BOND = 8463.2631 ANGLE = 22341.6410 DIHED = 32332.6793 VDWAALS = -24041.2121 EEL = -190580.1447 EGB = -62831.3526 1-4 VDW = 10676.9363 1-4 EEL = 146113.9594 RESTRAINT = 0.0000 ESURF = 983.1261 minimization completed, ENE= -.56541104E+05 RMS= 0.173839E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6633E+04 1.7337E+01 1.4384E+02 CG 24287 BOND = 8314.3507 ANGLE = 22255.6648 DIHED = 32414.6379 VDWAALS = -24044.2364 EEL = -191103.1614 EGB = -62543.4244 1-4 VDW = 10757.1773 1-4 EEL = 146331.3986 RESTRAINT = 0.0000 ESURF = 984.8845 minimization completed, ENE= -.56632708E+05 RMS= 0.173370E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6711E+04 1.7340E+01 1.2545E+02 C 29120 BOND = 8462.7973 ANGLE = 22123.5695 DIHED = 32267.4538 VDWAALS = -24096.5454 EEL = -191026.0448 EGB = -62532.3229 1-4 VDW = 10757.5421 1-4 EEL = 146355.4075 RESTRAINT = 0.0000 ESURF = 977.6326 minimization completed, ENE= -.56710510E+05 RMS= 0.173400E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6681E+04 1.7379E+01 1.3398E+02 CD 37114 BOND = 8468.4910 ANGLE = 22267.7033 DIHED = 32377.3166 VDWAALS = -24194.0519 EEL = -190661.3388 EGB = -62777.2296 1-4 VDW = 10701.8916 1-4 EEL = 146150.9440 RESTRAINT = 0.0000 ESURF = 984.8922 minimization completed, ENE= -.56681382E+05 RMS= 0.173795E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6611E+04 1.7385E+01 1.3092E+02 CZ 26470 BOND = 8582.4361 ANGLE = 22092.9367 DIHED = 32378.3506 VDWAALS = -24106.6588 EEL = -190642.0251 EGB = -62756.2881 1-4 VDW = 10707.3880 1-4 EEL = 146144.1563 RESTRAINT = 0.0000 ESURF = 988.4228 minimization completed, ENE= -.56611281E+05 RMS= 0.173850E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6818E+04 1.7251E+01 1.3528E+02 C 19528 BOND = 8347.9283 ANGLE = 22162.5878 DIHED = 32334.4289 VDWAALS = -24059.3506 EEL = -191211.7337 EGB = -62561.0856 1-4 VDW = 10819.5594 1-4 EEL = 146364.0418 RESTRAINT = 0.0000 ESURF = 985.2067 minimization completed, ENE= -.56818417E+05 RMS= 0.172506E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6565E+04 1.7373E+01 1.3455E+02 CA 22094 BOND = 8354.2198 ANGLE = 22315.6456 DIHED = 32357.3086 VDWAALS = -24103.0602 EEL = -191238.2317 EGB = -62267.3485 1-4 VDW = 10775.7703 1-4 EEL = 146253.4345 RESTRAINT = 0.0000 ESURF = 986.9324 minimization completed, ENE= -.56565329E+05 RMS= 0.173730E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6380E+04 1.7439E+01 1.3389E+02 CD 34119 BOND = 8452.7676 ANGLE = 22427.7756 DIHED = 32470.8850 VDWAALS = -24093.3925 EEL = -190997.4202 EGB = -62472.6666 1-4 VDW = 10729.2753 1-4 EEL = 146116.2232 RESTRAINT = 0.0000 ESURF = 986.3235 minimization completed, ENE= -.56380229E+05 RMS= 0.174394E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6614E+04 1.7350E+01 1.3398E+02 C 7599 BOND = 8355.3206 ANGLE = 22274.8282 DIHED = 32380.9018 VDWAALS = -24126.0957 EEL = -191007.0103 EGB = -62423.2906 1-4 VDW = 10746.8949 1-4 EEL = 146203.3602 RESTRAINT = 0.0000 ESURF = 980.7763 minimization completed, ENE= -.56614315E+05 RMS= 0.173495E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6831E+04 1.7261E+01 1.2255E+02 C 10184 BOND = 8302.1805 ANGLE = 22163.5276 DIHED = 32358.0703 VDWAALS = -24015.6339 EEL = -191244.7390 EGB = -62276.4845 1-4 VDW = 10748.7592 1-4 EEL = 146150.2129 RESTRAINT = 0.0000 ESURF = 982.9996 minimization completed, ENE= -.56831107E+05 RMS= 0.172610E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6726E+04 1.7276E+01 1.3264E+02 N 37643 BOND = 8349.5475 ANGLE = 22169.0883 DIHED = 32451.5180 VDWAALS = -24293.0560 EEL = -191005.9433 EGB = -62544.7637 1-4 VDW = 10723.8557 1-4 EEL = 146444.7053 RESTRAINT = 0.0000 ESURF = 979.5135 minimization completed, ENE= -.56725535E+05 RMS= 0.172764E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6662E+04 1.7393E+01 1.2842E+02 C 2477 BOND = 8439.2155 ANGLE = 22210.2328 DIHED = 32380.0976 VDWAALS = -24071.9679 EEL = -191384.8889 EGB = -62221.2752 1-4 VDW = 10733.5269 1-4 EEL = 146273.2691 RESTRAINT = 0.0000 ESURF = 979.6161 minimization completed, ENE= -.56662174E+05 RMS= 0.173933E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6438E+04 1.7357E+01 1.4002E+02 CD 29364 BOND = 8370.9261 ANGLE = 22306.8909 DIHED = 32541.6037 VDWAALS = -24109.3105 EEL = -191032.7928 EGB = -62648.5941 1-4 VDW = 10767.2082 1-4 EEL = 146387.7000 RESTRAINT = 0.0000 ESURF = 978.3984 minimization completed, ENE= -.56437970E+05 RMS= 0.173567E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6849E+04 1.7374E+01 1.2174E+02 C 120 BOND = 8448.4528 ANGLE = 22032.8238 DIHED = 32388.6125 VDWAALS = -24128.7798 EEL = -191474.0493 EGB = -62334.8295 1-4 VDW = 10807.4323 1-4 EEL = 146427.4882 RESTRAINT = 0.0000 ESURF = 984.0708 minimization completed, ENE= -.56848778E+05 RMS= 0.173741E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6674E+04 1.7430E+01 1.3099E+02 C 36665 BOND = 8419.2911 ANGLE = 22357.3983 DIHED = 32454.9563 VDWAALS = -24272.9285 EEL = -190963.3767 EGB = -62584.6314 1-4 VDW = 10712.3704 1-4 EEL = 146221.3108 RESTRAINT = 0.0000 ESURF = 982.0747 minimization completed, ENE= -.56673535E+05 RMS= 0.174297E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6580E+04 1.7299E+01 1.2086E+02 CA 32595 BOND = 8424.1310 ANGLE = 22225.5265 DIHED = 32391.1017 VDWAALS = -24058.8055 EEL = -191000.8742 EGB = -62572.3486 1-4 VDW = 10704.9494 1-4 EEL = 146323.5686 RESTRAINT = 0.0000 ESURF = 983.0847 minimization completed, ENE= -.56579666E+05 RMS= 0.172994E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6728E+04 1.7222E+01 1.3139E+02 C 20098 BOND = 8323.2253 ANGLE = 22191.9967 DIHED = 32384.3142 VDWAALS = -24139.0745 EEL = -190924.8025 EGB = -62748.8454 1-4 VDW = 10763.7379 1-4 EEL = 146436.8936 RESTRAINT = 0.0000 ESURF = 984.8128 minimization completed, ENE= -.56727742E+05 RMS= 0.172221E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6620E+04 1.7328E+01 1.3918E+02 C 19621 BOND = 8498.7341 ANGLE = 22231.3701 DIHED = 32333.3398 VDWAALS = -24090.8246 EEL = -191201.2582 EGB = -62399.2198 1-4 VDW = 10705.3460 1-4 EEL = 146317.9618 RESTRAINT = 0.0000 ESURF = 984.9726 minimization completed, ENE= -.56619578E+05 RMS= 0.173282E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6402E+04 1.7376E+01 1.6410E+02 C 25307 BOND = 8354.5102 ANGLE = 22276.6300 DIHED = 32514.4929 VDWAALS = -24095.6624 EEL = -191092.7721 EGB = -62519.8452 1-4 VDW = 10778.7454 1-4 EEL = 146397.8728 RESTRAINT = 0.0000 ESURF = 983.8162 minimization completed, ENE= -.56402212E+05 RMS= 0.173761E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6954E+04 1.7162E+01 1.4657E+02 C 8233 BOND = 8248.1981 ANGLE = 22160.6014 DIHED = 32358.6577 VDWAALS = -24145.5357 EEL = -191288.0953 EGB = -62331.1177 1-4 VDW = 10696.7762 1-4 EEL = 146365.1300 RESTRAINT = 0.0000 ESURF = 981.0913 minimization completed, ENE= -.56954294E+05 RMS= 0.171623E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6461E+04 1.7288E+01 1.3412E+02 CG 40462 BOND = 8346.8197 ANGLE = 22213.5252 DIHED = 32479.3118 VDWAALS = -24029.5381 EEL = -191141.0243 EGB = -62355.6358 1-4 VDW = 10779.9394 1-4 EEL = 146261.7841 RESTRAINT = 0.0000 ESURF = 983.7261 minimization completed, ENE= -.56461092E+05 RMS= 0.172879E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6507E+04 1.7344E+01 1.4982E+02 C 33538 BOND = 8334.4723 ANGLE = 22344.6328 DIHED = 32408.4291 VDWAALS = -24207.3445 EEL = -190369.6595 EGB = -62764.9358 1-4 VDW = 10734.2037 1-4 EEL = 146026.4206 RESTRAINT = 0.0000 ESURF = 987.1711 minimization completed, ENE= -.56506610E+05 RMS= 0.173441E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2864.31 ( 4.98% of Gen B) | Calc gb diag 13781.22 (23.94% of Gen B) | Calc gb off-diag 40910.94 (71.08% of Gen B) | Gen Born time 57556.48 (100.0% of Nonbo) | Nonbond force 57556.48 (100.0% of Force) | Bond/Angle/Dihedral 17.18 ( 0.03% of Force) | Force time 57573.69 (100.0% of Runmd) | Runmd Time 57573.69 (99.85% of Total) | Other 84.24 ( 0.15% of Total) | Total time 57658.05 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:34:07.014 on 10/17/2010 | Setup done at 07:34:08.789 on 10/17/2010 | Run done at 23:35:05.069 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:34:00 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.28 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.28 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6790E+04 1.7304E+01 1.2696E+02 C 41124 BOND = 8402.3760 ANGLE = 22197.1859 DIHED = 32346.1469 VDWAALS = -24042.9104 EEL = -190845.5876 EGB = -62739.1275 1-4 VDW = 10765.2213 1-4 EEL = 146135.5313 RESTRAINT = 0.0000 ESURF = 990.9830 minimization completed, ENE= -.56790181E+05 RMS= 0.173042E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6820E+04 1.7366E+01 1.2758E+02 C 28122 BOND = 8424.8884 ANGLE = 22350.2573 DIHED = 32282.9154 VDWAALS = -24150.3086 EEL = -191028.9548 EGB = -62555.9634 1-4 VDW = 10669.3269 1-4 EEL = 146194.5033 RESTRAINT = 0.0000 ESURF = 992.8504 minimization completed, ENE= -.56820485E+05 RMS= 0.173656E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6696E+04 1.7417E+01 1.2385E+02 CG 42468 BOND = 8441.9764 ANGLE = 22247.5785 DIHED = 32542.9856 VDWAALS = -24176.8265 EEL = -190458.9190 EGB = -63049.2601 1-4 VDW = 10725.4496 1-4 EEL = 146039.4247 RESTRAINT = 0.0000 ESURF = 991.9733 minimization completed, ENE= -.56695618E+05 RMS= 0.174171E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6632E+04 1.7246E+01 1.5456E+02 C 31913 BOND = 8332.4551 ANGLE = 22084.7065 DIHED = 32382.4995 VDWAALS = -24025.9696 EEL = -190955.4427 EGB = -62613.0478 1-4 VDW = 10806.7970 1-4 EEL = 146365.8429 RESTRAINT = 0.0000 ESURF = 989.8101 minimization completed, ENE= -.56632349E+05 RMS= 0.172463E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6361E+04 1.7299E+01 1.3706E+02 C 39114 BOND = 8445.0550 ANGLE = 22393.4724 DIHED = 32501.9541 VDWAALS = -24105.0551 EEL = -190691.2510 EGB = -62715.3739 1-4 VDW = 10730.9118 1-4 EEL = 146094.8729 RESTRAINT = 0.0000 ESURF = 984.5044 minimization completed, ENE= -.56360910E+05 RMS= 0.172989E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6985E+04 1.7249E+01 1.3887E+02 C 16462 BOND = 8360.7671 ANGLE = 22089.6405 DIHED = 32401.1231 VDWAALS = -24169.8733 EEL = -191023.6427 EGB = -62708.7686 1-4 VDW = 10730.2170 1-4 EEL = 146344.8268 RESTRAINT = 0.0000 ESURF = 990.8849 minimization completed, ENE= -.56984825E+05 RMS= 0.172487E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6639E+04 1.7404E+01 1.4431E+02 CG 18280 BOND = 8387.6745 ANGLE = 22340.0093 DIHED = 32443.0547 VDWAALS = -24181.3596 EEL = -190901.7628 EGB = -62545.6695 1-4 VDW = 10717.4396 1-4 EEL = 146107.3085 RESTRAINT = 0.0000 ESURF = 993.9566 minimization completed, ENE= -.56639349E+05 RMS= 0.174044E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6423E+04 1.7448E+01 1.3007E+02 C 32533 BOND = 8461.2137 ANGLE = 22370.1828 DIHED = 32452.6612 VDWAALS = -24020.5645 EEL = -190972.5214 EGB = -62772.5619 1-4 VDW = 10764.8018 1-4 EEL = 146302.3776 RESTRAINT = 0.0000 ESURF = 991.5974 minimization completed, ENE= -.56422813E+05 RMS= 0.174484E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6717E+04 1.7283E+01 1.2274E+02 C 18393 BOND = 8268.3872 ANGLE = 22199.8490 DIHED = 32436.2418 VDWAALS = -24215.9145 EEL = -190469.3196 EGB = -62926.2889 1-4 VDW = 10783.7130 1-4 EEL = 146216.9070 RESTRAINT = 0.0000 ESURF = 989.2925 minimization completed, ENE= -.56717133E+05 RMS= 0.172829E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6786E+04 1.7257E+01 1.2932E+02 N 26108 BOND = 8249.8879 ANGLE = 22142.1416 DIHED = 32342.1023 VDWAALS = -24085.0875 EEL = -190559.1246 EGB = -63056.5821 1-4 VDW = 10802.3518 1-4 EEL = 146393.4839 RESTRAINT = 0.0000 ESURF = 985.1099 minimization completed, ENE= -.56785717E+05 RMS= 0.172570E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6429E+04 1.7394E+01 1.2489E+02 CG 17299 BOND = 8422.2801 ANGLE = 22286.1968 DIHED = 32370.9932 VDWAALS = -24130.7031 EEL = -190267.6240 EGB = -63140.3055 1-4 VDW = 10747.2829 1-4 EEL = 146297.8314 RESTRAINT = 0.0000 ESURF = 984.8829 minimization completed, ENE= -.56429165E+05 RMS= 0.173943E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6456E+04 1.7301E+01 1.2856E+02 C 4333 BOND = 8410.6404 ANGLE = 22266.4307 DIHED = 32441.3590 VDWAALS = -24116.5915 EEL = -190540.2603 EGB = -62886.6251 1-4 VDW = 10743.0494 1-4 EEL = 146235.7556 RESTRAINT = 0.0000 ESURF = 990.4974 minimization completed, ENE= -.56455744E+05 RMS= 0.173011E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6415E+04 1.7483E+01 1.1796E+02 C 1677 BOND = 8560.9883 ANGLE = 22342.6269 DIHED = 32375.0336 VDWAALS = -23999.7270 EEL = -190773.0221 EGB = -62818.1881 1-4 VDW = 10725.0006 1-4 EEL = 146186.9568 RESTRAINT = 0.0000 ESURF = 984.9059 minimization completed, ENE= -.56415425E+05 RMS= 0.174830E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6481E+04 1.7383E+01 1.3447E+02 C 31104 BOND = 8476.5422 ANGLE = 22360.5252 DIHED = 32374.9863 VDWAALS = -24235.4073 EEL = -190843.3452 EGB = -62597.9247 1-4 VDW = 10750.4233 1-4 EEL = 146256.2054 RESTRAINT = 0.0000 ESURF = 977.3548 minimization completed, ENE= -.56480640E+05 RMS= 0.173829E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6319E+04 1.7402E+01 1.1824E+02 N 38623 BOND = 8482.8174 ANGLE = 22390.6543 DIHED = 32471.2934 VDWAALS = -24075.7999 EEL = -190403.6896 EGB = -63025.6754 1-4 VDW = 10710.7645 1-4 EEL = 146146.5839 RESTRAINT = 0.0000 ESURF = 984.2455 minimization completed, ENE= -.56318806E+05 RMS= 0.174018E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6738E+04 1.7302E+01 1.2425E+02 C 45303 BOND = 8370.0508 ANGLE = 22252.3956 DIHED = 32367.2801 VDWAALS = -24287.4709 EEL = -190471.3330 EGB = -62728.7326 1-4 VDW = 10714.7634 1-4 EEL = 146065.4080 RESTRAINT = 0.0000 ESURF = 979.8787 minimization completed, ENE= -.56737760E+05 RMS= 0.173024E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6495E+04 1.7271E+01 1.2159E+02 CA 29066 BOND = 8357.8782 ANGLE = 22408.4658 DIHED = 32368.3311 VDWAALS = -24144.7220 EEL = -190251.7266 EGB = -63182.1748 1-4 VDW = 10724.5567 1-4 EEL = 146239.7117 RESTRAINT = 0.0000 ESURF = 984.3069 minimization completed, ENE= -.56495373E+05 RMS= 0.172712E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6214E+04 1.7464E+01 1.3588E+02 C 39828 BOND = 8447.4194 ANGLE = 22228.2381 DIHED = 32540.0205 VDWAALS = -24259.6765 EEL = -190167.6388 EGB = -63073.1071 1-4 VDW = 10856.3417 1-4 EEL = 146234.8533 RESTRAINT = 0.0000 ESURF = 979.9564 minimization completed, ENE= -.56213593E+05 RMS= 0.174635E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6363E+04 1.7329E+01 1.3455E+02 C 8477 BOND = 8427.8524 ANGLE = 22354.6974 DIHED = 32373.1282 VDWAALS = -24160.1310 EEL = -190850.7314 EGB = -62622.5573 1-4 VDW = 10810.1378 1-4 EEL = 146320.5040 RESTRAINT = 0.0000 ESURF = 983.9821 minimization completed, ENE= -.56363118E+05 RMS= 0.173293E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6646E+04 1.7320E+01 1.3130E+02 C 2219 BOND = 8261.4867 ANGLE = 22309.6960 DIHED = 32294.8400 VDWAALS = -24058.1916 EEL = -190835.0243 EGB = -62901.9621 1-4 VDW = 10810.2465 1-4 EEL = 146494.7778 RESTRAINT = 0.0000 ESURF = 978.3757 minimization completed, ENE= -.56645755E+05 RMS= 0.173203E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6594E+04 1.7303E+01 1.2408E+02 CZ 21740 BOND = 8346.6038 ANGLE = 22211.9077 DIHED = 32509.1891 VDWAALS = -24116.3844 EEL = -190808.7882 EGB = -62728.4840 1-4 VDW = 10721.6211 1-4 EEL = 146285.9831 RESTRAINT = 0.0000 ESURF = 984.5503 minimization completed, ENE= -.56593801E+05 RMS= 0.173033E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6615E+04 1.7300E+01 1.2229E+02 C 7991 BOND = 8335.2774 ANGLE = 22229.9557 DIHED = 32416.0086 VDWAALS = -24082.6605 EEL = -190814.7787 EGB = -62492.4484 1-4 VDW = 10733.7857 1-4 EEL = 146073.9471 RESTRAINT = 0.0000 ESURF = 986.0575 minimization completed, ENE= -.56614856E+05 RMS= 0.173003E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6333E+04 1.7342E+01 1.3281E+02 C 45381 BOND = 8386.5356 ANGLE = 22434.6895 DIHED = 32507.9835 VDWAALS = -24191.5685 EEL = -190602.1573 EGB = -62801.0786 1-4 VDW = 10726.2046 1-4 EEL = 146222.3035 RESTRAINT = 0.0000 ESURF = 984.4278 minimization completed, ENE= -.56332660E+05 RMS= 0.173421E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6195E+04 1.7463E+01 1.3180E+02 CD 33477 BOND = 8408.9276 ANGLE = 22495.8328 DIHED = 32474.8201 VDWAALS = -24026.2793 EEL = -191094.4217 EGB = -62390.0550 1-4 VDW = 10731.4050 1-4 EEL = 146222.6179 RESTRAINT = 0.0000 ESURF = 982.6322 minimization completed, ENE= -.56194520E+05 RMS= 0.174629E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6727E+04 1.7330E+01 1.2961E+02 CG 25555 BOND = 8405.9516 ANGLE = 22146.1291 DIHED = 32342.7168 VDWAALS = -24175.2161 EEL = -190524.7638 EGB = -62819.4352 1-4 VDW = 10680.6366 1-4 EEL = 146232.4832 RESTRAINT = 0.0000 ESURF = 984.2422 minimization completed, ENE= -.56727255E+05 RMS= 0.173298E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2867.15 ( 4.99% of Gen B) | Calc gb diag 13893.19 (24.19% of Gen B) | Calc gb off-diag 40670.65 (70.82% of Gen B) | Gen Born time 57431.30 (100.0% of Nonbo) | Nonbond force 57431.30 (100.0% of Force) | Bond/Angle/Dihedral 15.55 ( 0.03% of Force) | Force time 57446.88 (100.0% of Runmd) | Runmd Time 57446.88 (99.85% of Total) | Other 84.54 ( 0.15% of Total) | Total time 57531.54 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:34:00.458 on 10/17/2010 | Setup done at 07:34:03.463 on 10/17/2010 | Run done at 23:32:52.001 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:33:53 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.27 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.27 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6400E+04 1.7361E+01 1.4441E+02 CD 8988 BOND = 8449.6065 ANGLE = 22289.5824 DIHED = 32413.4466 VDWAALS = -24113.8910 EEL = -190451.7379 EGB = -62916.6641 1-4 VDW = 10704.4551 1-4 EEL = 146234.9590 RESTRAINT = 0.0000 ESURF = 990.4854 minimization completed, ENE= -.56399758E+05 RMS= 0.173609E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6480E+04 1.7292E+01 1.4957E+02 CD 25395 BOND = 8388.5800 ANGLE = 22285.8285 DIHED = 32455.1482 VDWAALS = -24081.9902 EEL = -190026.4018 EGB = -63320.0237 1-4 VDW = 10743.8783 1-4 EEL = 146083.2636 RESTRAINT = 0.0000 ESURF = 992.1836 minimization completed, ENE= -.56479534E+05 RMS= 0.172925E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6545E+04 1.7302E+01 1.2109E+02 CG 46246 BOND = 8359.0660 ANGLE = 22253.1011 DIHED = 32394.6788 VDWAALS = -24189.8680 EEL = -190519.7627 EGB = -62657.3132 1-4 VDW = 10668.9935 1-4 EEL = 146162.8833 RESTRAINT = 0.0000 ESURF = 983.6399 minimization completed, ENE= -.56544581E+05 RMS= 0.173019E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6591E+04 1.7295E+01 1.1682E+02 C 24591 BOND = 8261.9832 ANGLE = 22280.8434 DIHED = 32391.4081 VDWAALS = -23969.9418 EEL = -190290.8639 EGB = -63152.1814 1-4 VDW = 10806.3271 1-4 EEL = 146088.4520 RESTRAINT = 0.0000 ESURF = 993.1477 minimization completed, ENE= -.56590826E+05 RMS= 0.172947E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6315E+04 1.7440E+01 1.4937E+02 C 29865 BOND = 8456.3527 ANGLE = 22190.7845 DIHED = 32392.5002 VDWAALS = -24039.3531 EEL = -190180.6067 EGB = -63219.3702 1-4 VDW = 10819.0183 1-4 EEL = 146276.8694 RESTRAINT = 0.0000 ESURF = 988.6492 minimization completed, ENE= -.56315156E+05 RMS= 0.174402E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6328E+04 1.7391E+01 1.3405E+02 C 42200 BOND = 8401.1971 ANGLE = 22469.1365 DIHED = 32392.7512 VDWAALS = -24122.3351 EEL = -190193.2596 EGB = -63164.9804 1-4 VDW = 10724.5454 1-4 EEL = 146176.5793 RESTRAINT = 0.0000 ESURF = 988.7105 minimization completed, ENE= -.56327655E+05 RMS= 0.173912E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6520E+04 1.7336E+01 1.4156E+02 C 18842 BOND = 8385.2585 ANGLE = 22357.4503 DIHED = 32332.5179 VDWAALS = -24161.2204 EEL = -190096.8922 EGB = -63088.9818 1-4 VDW = 10680.2067 1-4 EEL = 146082.5469 RESTRAINT = 0.0000 ESURF = 989.0949 minimization completed, ENE= -.56520019E+05 RMS= 0.173361E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6633E+04 1.7395E+01 1.5426E+02 C 36068 BOND = 8441.3080 ANGLE = 22276.3243 DIHED = 32428.7651 VDWAALS = -24318.4281 EEL = -190033.0375 EGB = -63136.5636 1-4 VDW = 10648.2268 1-4 EEL = 146074.9126 RESTRAINT = 0.0000 ESURF = 985.6088 minimization completed, ENE= -.56632884E+05 RMS= 0.173947E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6493E+04 1.7341E+01 1.1765E+02 C 5993 BOND = 8413.4002 ANGLE = 22213.9521 DIHED = 32403.8106 VDWAALS = -24271.2770 EEL = -189868.4494 EGB = -63325.2909 1-4 VDW = 10746.3444 1-4 EEL = 146209.6003 RESTRAINT = 0.0000 ESURF = 984.7580 minimization completed, ENE= -.56493152E+05 RMS= 0.173411E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6534E+04 1.7323E+01 1.5251E+02 CG 24466 BOND = 8397.6660 ANGLE = 22262.9185 DIHED = 32490.8524 VDWAALS = -24231.4904 EEL = -190012.5481 EGB = -63112.4945 1-4 VDW = 10657.4025 1-4 EEL = 146020.7922 RESTRAINT = 0.0000 ESURF = 992.7041 minimization completed, ENE= -.56534197E+05 RMS= 0.173233E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6178E+04 1.7471E+01 1.4595E+02 C 17157 BOND = 8446.7954 ANGLE = 22487.3652 DIHED = 32430.5730 VDWAALS = -24213.5875 EEL = -189803.5227 EGB = -63463.7922 1-4 VDW = 10769.8695 1-4 EEL = 146179.8116 RESTRAINT = 0.0000 ESURF = 988.2686 minimization completed, ENE= -.56178219E+05 RMS= 0.174709E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6531E+04 1.7256E+01 1.2631E+02 C 33089 BOND = 8479.5398 ANGLE = 22251.9797 DIHED = 32517.9127 VDWAALS = -24281.6819 EEL = -190104.2180 EGB = -63213.8769 1-4 VDW = 10735.6149 1-4 EEL = 146093.1472 RESTRAINT = 0.0000 ESURF = 990.4025 minimization completed, ENE= -.56531180E+05 RMS= 0.172563E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6714E+04 1.7216E+01 1.5048E+02 C 14173 BOND = 8400.9062 ANGLE = 22287.5939 DIHED = 32364.9050 VDWAALS = -24259.4630 EEL = -190335.0424 EGB = -63031.1700 1-4 VDW = 10695.0032 1-4 EEL = 146175.5138 RESTRAINT = 0.0000 ESURF = 988.1003 minimization completed, ENE= -.56713653E+05 RMS= 0.172158E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6460E+04 1.7276E+01 1.4718E+02 C 19280 BOND = 8418.4363 ANGLE = 22299.8097 DIHED = 32462.4868 VDWAALS = -24077.5828 EEL = -190277.6151 EGB = -63162.0741 1-4 VDW = 10742.2395 1-4 EEL = 146141.5134 RESTRAINT = 0.0000 ESURF = 992.4967 minimization completed, ENE= -.56460290E+05 RMS= 0.172755E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6436E+04 1.7350E+01 1.6943E+02 CD 20967 BOND = 8421.6453 ANGLE = 22325.2753 DIHED = 32421.5969 VDWAALS = -24119.5951 EEL = -190344.6759 EGB = -62957.8047 1-4 VDW = 10763.4264 1-4 EEL = 146065.4854 RESTRAINT = 0.0000 ESURF = 989.0248 minimization completed, ENE= -.56435622E+05 RMS= 0.173502E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6771E+04 1.7365E+01 1.1674E+02 C 44162 BOND = 8403.8776 ANGLE = 22314.7911 DIHED = 32394.7261 VDWAALS = -24166.6579 EEL = -190216.7224 EGB = -63188.0428 1-4 VDW = 10660.9913 1-4 EEL = 146030.3457 RESTRAINT = 0.0000 ESURF = 995.9904 minimization completed, ENE= -.56770701E+05 RMS= 0.173649E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6552E+04 1.7296E+01 1.3952E+02 CD1 40171 BOND = 8413.4565 ANGLE = 22207.4284 DIHED = 32423.4855 VDWAALS = -24099.9420 EEL = -190631.1939 EGB = -62737.7934 1-4 VDW = 10794.9633 1-4 EEL = 146088.4494 RESTRAINT = 0.0000 ESURF = 989.3369 minimization completed, ENE= -.56551809E+05 RMS= 0.172959E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6496E+04 1.7459E+01 1.3479E+02 C 44514 BOND = 8490.7539 ANGLE = 22487.4617 DIHED = 32453.6934 VDWAALS = -24164.5474 EEL = -190538.6008 EGB = -62864.3173 1-4 VDW = 10646.1017 1-4 EEL = 146001.6337 RESTRAINT = 0.0000 ESURF = 991.8879 minimization completed, ENE= -.56495933E+05 RMS= 0.174591E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6544E+04 1.7419E+01 1.3783E+02 C 5579 BOND = 8483.4996 ANGLE = 22286.6740 DIHED = 32435.8478 VDWAALS = -24128.0616 EEL = -190385.1836 EGB = -63065.5577 1-4 VDW = 10715.6654 1-4 EEL = 146122.2463 RESTRAINT = 0.0000 ESURF = 990.9457 minimization completed, ENE= -.56543924E+05 RMS= 0.174191E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6667E+04 1.7254E+01 1.2501E+02 C 13741 BOND = 8391.4646 ANGLE = 22235.8835 DIHED = 32442.4895 VDWAALS = -24207.3667 EEL = -190538.3853 EGB = -63005.0757 1-4 VDW = 10744.8817 1-4 EEL = 146283.2241 RESTRAINT = 0.0000 ESURF = 985.8866 minimization completed, ENE= -.56666998E+05 RMS= 0.172538E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6408E+04 1.7449E+01 1.3516E+02 CD 30709 BOND = 8460.4791 ANGLE = 22341.6684 DIHED = 32412.0216 VDWAALS = -24137.8384 EEL = -190523.5173 EGB = -62693.0753 1-4 VDW = 10726.5055 1-4 EEL = 146018.5203 RESTRAINT = 0.0000 ESURF = 986.9470 minimization completed, ENE= -.56408289E+05 RMS= 0.174495E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6421E+04 1.7411E+01 1.4005E+02 CD 36087 BOND = 8476.3681 ANGLE = 22148.5112 DIHED = 32425.1227 VDWAALS = -24055.6113 EEL = -190359.7811 EGB = -62904.3138 1-4 VDW = 10718.4020 1-4 EEL = 146134.9562 RESTRAINT = 0.0000 ESURF = 994.8786 minimization completed, ENE= -.56421467E+05 RMS= 0.174111E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6744E+04 1.7289E+01 1.3049E+02 CG 30888 BOND = 8355.0060 ANGLE = 22129.1077 DIHED = 32445.6865 VDWAALS = -24056.2023 EEL = -190812.0649 EGB = -62631.5075 1-4 VDW = 10678.0434 1-4 EEL = 146158.5965 RESTRAINT = 0.0000 ESURF = 989.5056 minimization completed, ENE= -.56743829E+05 RMS= 0.172889E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6579E+04 1.7323E+01 1.4369E+02 C 519 BOND = 8267.1783 ANGLE = 22445.2890 DIHED = 32411.7338 VDWAALS = -24163.1916 EEL = -190810.0618 EGB = -62619.9701 1-4 VDW = 10729.8181 1-4 EEL = 146168.8491 RESTRAINT = 0.0000 ESURF = 991.0295 minimization completed, ENE= -.56579326E+05 RMS= 0.173227E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6632E+04 1.7330E+01 1.2244E+02 CE1 7107 BOND = 8380.2742 ANGLE = 22292.1641 DIHED = 32373.4020 VDWAALS = -23989.9039 EEL = -190483.6640 EGB = -62882.1546 1-4 VDW = 10662.0066 1-4 EEL = 146027.2483 RESTRAINT = 0.0000 ESURF = 988.2678 minimization completed, ENE= -.56632359E+05 RMS= 0.173302E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2866.30 ( 4.97% of Gen B) | Calc gb diag 13721.00 (23.80% of Gen B) | Calc gb off-diag 41070.80 (71.23% of Gen B) | Gen Born time 57658.11 (100.0% of Nonbo) | Nonbond force 57658.11 (100.0% of Force) | Bond/Angle/Dihedral 17.52 ( 0.03% of Force) | Force time 57675.96 (100.0% of Runmd) | Runmd Time 57675.96 (99.85% of Total) | Other 84.58 ( 0.15% of Total) | Total time 57760.66 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:33:53.417 on 10/17/2010 | Setup done at 07:33:56.209 on 10/17/2010 | Run done at 23:36:34.081 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:33:47 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.26 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.26 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6374E+04 1.7302E+01 1.1657E+02 C 44896 BOND = 8461.7221 ANGLE = 22391.2787 DIHED = 32463.9662 VDWAALS = -24127.6198 EEL = -190376.5655 EGB = -63136.5395 1-4 VDW = 10726.6476 1-4 EEL = 146233.0428 RESTRAINT = 0.0000 ESURF = 990.0847 minimization completed, ENE= -.56373983E+05 RMS= 0.173023E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6449E+04 1.7363E+01 1.3209E+02 C 14112 BOND = 8471.7330 ANGLE = 22227.3394 DIHED = 32442.3119 VDWAALS = -24153.7135 EEL = -190084.9132 EGB = -63389.1468 1-4 VDW = 10725.6449 1-4 EEL = 146323.6844 RESTRAINT = 0.0000 ESURF = 988.0362 minimization completed, ENE= -.56449024E+05 RMS= 0.173626E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6557E+04 1.7332E+01 1.3380E+02 CG 42938 BOND = 8274.0739 ANGLE = 22325.9517 DIHED = 32393.6725 VDWAALS = -24119.1074 EEL = -190565.7259 EGB = -63004.5628 1-4 VDW = 10758.5977 1-4 EEL = 146390.9387 RESTRAINT = 0.0000 ESURF = 989.3297 minimization completed, ENE= -.56556832E+05 RMS= 0.173319E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6682E+04 1.7344E+01 1.4219E+02 CA 40185 BOND = 8359.3578 ANGLE = 22287.4768 DIHED = 32356.6305 VDWAALS = -24015.5170 EEL = -190643.7063 EGB = -63006.5301 1-4 VDW = 10665.8076 1-4 EEL = 146319.9441 RESTRAINT = 0.0000 ESURF = 994.1412 minimization completed, ENE= -.56682395E+05 RMS= 0.173440E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6641E+04 1.7349E+01 1.4044E+02 C 31453 BOND = 8477.6513 ANGLE = 22258.4041 DIHED = 32427.0416 VDWAALS = -24164.9488 EEL = -190486.0263 EGB = -63090.9977 1-4 VDW = 10723.7068 1-4 EEL = 146219.6331 RESTRAINT = 0.0000 ESURF = 994.2756 minimization completed, ENE= -.56641260E+05 RMS= 0.173487E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6500E+04 1.7248E+01 1.1877E+02 N 3092 BOND = 8359.4147 ANGLE = 22247.7181 DIHED = 32383.6096 VDWAALS = -23956.0622 EEL = -190132.8131 EGB = -63281.5151 1-4 VDW = 10746.8678 1-4 EEL = 146141.4808 RESTRAINT = 0.0000 ESURF = 990.9572 minimization completed, ENE= -.56500342E+05 RMS= 0.172481E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6277E+04 1.7495E+01 1.3650E+02 C 4921 BOND = 8498.8084 ANGLE = 22465.3974 DIHED = 32436.0919 VDWAALS = -24186.9713 EEL = -190270.5330 EGB = -63018.9673 1-4 VDW = 10687.6711 1-4 EEL = 146116.8663 RESTRAINT = 0.0000 ESURF = 994.2419 minimization completed, ENE= -.56277395E+05 RMS= 0.174951E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6758E+04 1.7259E+01 1.3151E+02 C 46511 BOND = 8402.8426 ANGLE = 22140.4006 DIHED = 32291.1962 VDWAALS = -24069.1610 EEL = -190130.0504 EGB = -63155.2023 1-4 VDW = 10670.0048 1-4 EEL = 146097.6847 RESTRAINT = 0.0000 ESURF = 994.6885 minimization completed, ENE= -.56757596E+05 RMS= 0.172590E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6374E+04 1.7302E+01 1.2684E+02 N 3580 BOND = 8393.7322 ANGLE = 22429.7739 DIHED = 32460.2832 VDWAALS = -24040.8868 EEL = -190367.2155 EGB = -63108.8781 1-4 VDW = 10651.6598 1-4 EEL = 146212.2047 RESTRAINT = 0.0000 ESURF = 995.7041 minimization completed, ENE= -.56373622E+05 RMS= 0.173019E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6438E+04 1.7390E+01 1.5424E+02 CZ 15941 BOND = 8486.4356 ANGLE = 22349.2459 DIHED = 32344.3143 VDWAALS = -24154.3922 EEL = -190758.8617 EGB = -62748.8880 1-4 VDW = 10742.9658 1-4 EEL = 146308.0074 RESTRAINT = 0.0000 ESURF = 992.9514 minimization completed, ENE= -.56438222E+05 RMS= 0.173895E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6726E+04 1.7134E+01 1.1680E+02 N 27430 BOND = 8170.2587 ANGLE = 22207.6119 DIHED = 32504.2761 VDWAALS = -24091.3416 EEL = -190431.3736 EGB = -63024.1444 1-4 VDW = 10684.7602 1-4 EEL = 146261.3400 RESTRAINT = 0.0000 ESURF = 993.1067 minimization completed, ENE= -.56725506E+05 RMS= 0.171342E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6419E+04 1.7337E+01 1.4141E+02 C 36815 BOND = 8421.9728 ANGLE = 22302.3871 DIHED = 32434.6467 VDWAALS = -24173.3611 EEL = -190200.5751 EGB = -63099.8080 1-4 VDW = 10737.5126 1-4 EEL = 146164.7092 RESTRAINT = 0.0000 ESURF = 993.7337 minimization completed, ENE= -.56418782E+05 RMS= 0.173369E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6597E+04 1.7375E+01 1.4542E+02 C 18140 BOND = 8377.7160 ANGLE = 22269.5973 DIHED = 32420.4684 VDWAALS = -24015.6902 EEL = -190849.5512 EGB = -62998.2193 1-4 VDW = 10705.0239 1-4 EEL = 146498.6219 RESTRAINT = 0.0000 ESURF = 995.0600 minimization completed, ENE= -.56596973E+05 RMS= 0.173751E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6703E+04 1.7320E+01 1.4401E+02 C 31738 BOND = 8348.4952 ANGLE = 22264.8507 DIHED = 32288.4547 VDWAALS = -24112.4603 EEL = -190882.7974 EGB = -62745.1556 1-4 VDW = 10828.3681 1-4 EEL = 146313.1819 RESTRAINT = 0.0000 ESURF = 994.1498 minimization completed, ENE= -.56702913E+05 RMS= 0.173199E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6377E+04 1.7376E+01 1.4354E+02 C 42702 BOND = 8332.0915 ANGLE = 22480.3593 DIHED = 32450.5641 VDWAALS = -24057.2020 EEL = -190650.2343 EGB = -62808.7495 1-4 VDW = 10696.0790 1-4 EEL = 146185.2109 RESTRAINT = 0.0000 ESURF = 994.5556 minimization completed, ENE= -.56377326E+05 RMS= 0.173761E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6834E+04 1.7277E+01 1.4262E+02 N 13808 BOND = 8287.3966 ANGLE = 21951.5746 DIHED = 32377.1962 VDWAALS = -24099.6456 EEL = -190552.2742 EGB = -62983.4586 1-4 VDW = 10798.3820 1-4 EEL = 146390.9426 RESTRAINT = 0.0000 ESURF = 996.1007 minimization completed, ENE= -.56833786E+05 RMS= 0.172774E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6544E+04 1.7333E+01 1.2367E+02 C 8670 BOND = 8409.1813 ANGLE = 22275.8711 DIHED = 32340.6415 VDWAALS = -24140.4808 EEL = -190396.3464 EGB = -63066.4154 1-4 VDW = 10762.8897 1-4 EEL = 146270.3186 RESTRAINT = 0.0000 ESURF = 1000.1719 minimization completed, ENE= -.56544168E+05 RMS= 0.173327E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6065E+04 1.7358E+01 1.3307E+02 CD 37834 BOND = 8383.9724 ANGLE = 22359.4351 DIHED = 32437.7782 VDWAALS = -24066.7851 EEL = -190173.1564 EGB = -63176.0326 1-4 VDW = 10810.6786 1-4 EEL = 146361.6315 RESTRAINT = 0.0000 ESURF = 997.2787 minimization completed, ENE= -.56065200E+05 RMS= 0.173584E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6399E+04 1.7298E+01 1.2743E+02 C 20015 BOND = 8446.3257 ANGLE = 22196.6588 DIHED = 32528.1745 VDWAALS = -24208.0356 EEL = -189526.3392 EGB = -63690.6431 1-4 VDW = 10698.4979 1-4 EEL = 146157.8739 RESTRAINT = 0.0000 ESURF = 998.0329 minimization completed, ENE= -.56399454E+05 RMS= 0.172981E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6366E+04 1.7371E+01 1.4554E+02 C 18038 BOND = 8463.6326 ANGLE = 22329.5285 DIHED = 32359.3298 VDWAALS = -24013.8853 EEL = -190380.0926 EGB = -63069.8986 1-4 VDW = 10659.2799 1-4 EEL = 146292.5759 RESTRAINT = 0.0000 ESURF = 993.5333 minimization completed, ENE= -.56365997E+05 RMS= 0.173709E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6267E+04 1.7357E+01 1.2596E+02 C 1978 BOND = 8447.4462 ANGLE = 22386.7314 DIHED = 32501.1878 VDWAALS = -24046.5269 EEL = -190215.0036 EGB = -63300.6103 1-4 VDW = 10707.7262 1-4 EEL = 146255.0377 RESTRAINT = 0.0000 ESURF = 997.0856 minimization completed, ENE= -.56266926E+05 RMS= 0.173567E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6551E+04 1.7318E+01 1.4186E+02 C 38023 BOND = 8392.0279 ANGLE = 22072.3789 DIHED = 32505.2014 VDWAALS = -24057.4937 EEL = -190077.0475 EGB = -63404.5115 1-4 VDW = 10717.0008 1-4 EEL = 146304.7037 RESTRAINT = 0.0000 ESURF = 996.9382 minimization completed, ENE= -.56550802E+05 RMS= 0.173184E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6502E+04 1.7236E+01 1.3410E+02 C 14713 BOND = 8366.1491 ANGLE = 22110.8340 DIHED = 32462.9626 VDWAALS = -24053.8946 EEL = -190263.8613 EGB = -63049.2117 1-4 VDW = 10759.5687 1-4 EEL = 146169.4966 RESTRAINT = 0.0000 ESURF = 996.2724 minimization completed, ENE= -.56501684E+05 RMS= 0.172360E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6429E+04 1.7325E+01 1.3184E+02 C 8719 BOND = 8260.4953 ANGLE = 22500.0827 DIHED = 32413.1786 VDWAALS = -24049.9665 EEL = -190546.9135 EGB = -62926.0964 1-4 VDW = 10654.6171 1-4 EEL = 146274.9561 RESTRAINT = 0.0000 ESURF = 990.1629 minimization completed, ENE= -.56429484E+05 RMS= 0.173251E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6367E+04 1.7392E+01 1.5054E+02 C 30304 BOND = 8372.2002 ANGLE = 22320.5261 DIHED = 32449.7064 VDWAALS = -23976.7435 EEL = -190544.2032 EGB = -62970.0305 1-4 VDW = 10735.2559 1-4 EEL = 146252.8070 RESTRAINT = 0.0000 ESURF = 993.3293 minimization completed, ENE= -.56367152E+05 RMS= 0.173918E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2859.50 ( 4.97% of Gen B) | Calc gb diag 13854.02 (24.08% of Gen B) | Calc gb off-diag 40817.19 (70.95% of Gen B) | Gen Born time 57530.72 (100.0% of Nonbo) | Nonbond force 57530.72 (100.0% of Force) | Bond/Angle/Dihedral 17.19 ( 0.03% of Force) | Force time 57547.93 (100.0% of Runmd) | Runmd Time 57547.93 (99.85% of Total) | Other 84.04 ( 0.15% of Total) | Total time 57632.10 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:33:47.074 on 10/17/2010 | Setup done at 07:33:50.477 on 10/17/2010 | Run done at 23:34:19.177 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:33:40 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.25 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.25 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6548E+04 1.7365E+01 1.1548E+02 C 41505 BOND = 8458.1926 ANGLE = 22265.1578 DIHED = 32431.1209 VDWAALS = -24155.8226 EEL = -190550.4395 EGB = -62886.0761 1-4 VDW = 10708.1292 1-4 EEL = 146188.1249 RESTRAINT = 0.0000 ESURF = 993.1961 minimization completed, ENE= -.56548417E+05 RMS= 0.173649E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6523E+04 1.7395E+01 1.3272E+02 CD2 18575 BOND = 8538.3267 ANGLE = 22242.3098 DIHED = 32367.1062 VDWAALS = -24185.9604 EEL = -189869.5311 EGB = -63356.2429 1-4 VDW = 10682.4352 1-4 EEL = 146069.7294 RESTRAINT = 0.0000 ESURF = 989.0806 minimization completed, ENE= -.56522747E+05 RMS= 0.173951E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6327E+04 1.7331E+01 1.3572E+02 C 39196 BOND = 8489.0351 ANGLE = 22323.8681 DIHED = 32406.7490 VDWAALS = -24064.2900 EEL = -190800.1691 EGB = -62534.9950 1-4 VDW = 10703.4592 1-4 EEL = 146159.2022 RESTRAINT = 0.0000 ESURF = 990.0858 minimization completed, ENE= -.56327055E+05 RMS= 0.173312E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6825E+04 1.7234E+01 1.2939E+02 C 22071 BOND = 8434.3708 ANGLE = 22036.5077 DIHED = 32411.1361 VDWAALS = -24095.2546 EEL = -190423.9729 EGB = -63154.6649 1-4 VDW = 10717.0904 1-4 EEL = 146256.7241 RESTRAINT = 0.0000 ESURF = 993.4884 minimization completed, ENE= -.56824575E+05 RMS= 0.172345E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6744E+04 1.7330E+01 1.3845E+02 C 39732 BOND = 8524.8306 ANGLE = 22195.7417 DIHED = 32379.4060 VDWAALS = -24085.6446 EEL = -190532.7487 EGB = -63077.8759 1-4 VDW = 10684.0543 1-4 EEL = 146177.0106 RESTRAINT = 0.0000 ESURF = 991.6181 minimization completed, ENE= -.56743608E+05 RMS= 0.173298E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6776E+04 1.7341E+01 1.2179E+02 CZ 43160 BOND = 8378.1030 ANGLE = 22279.7598 DIHED = 32301.1674 VDWAALS = -24127.1231 EEL = -190601.9286 EGB = -62960.9577 1-4 VDW = 10739.0734 1-4 EEL = 146224.6031 RESTRAINT = 0.0000 ESURF = 991.0128 minimization completed, ENE= -.56776290E+05 RMS= 0.173408E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6413E+04 1.7292E+01 1.2304E+02 C 6087 BOND = 8317.7987 ANGLE = 22402.6063 DIHED = 32483.7748 VDWAALS = -24181.5232 EEL = -190086.2113 EGB = -63261.6193 1-4 VDW = 10797.4881 1-4 EEL = 146121.1600 RESTRAINT = 0.0000 ESURF = 993.0728 minimization completed, ENE= -.56413453E+05 RMS= 0.172919E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6438E+04 1.7302E+01 1.3086E+02 C 25908 BOND = 8399.1646 ANGLE = 22234.0900 DIHED = 32419.2030 VDWAALS = -24048.1591 EEL = -190745.9456 EGB = -62932.9953 1-4 VDW = 10791.4824 1-4 EEL = 146455.8260 RESTRAINT = 0.0000 ESURF = 989.4452 minimization completed, ENE= -.56437889E+05 RMS= 0.173018E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6861E+04 1.7229E+01 1.2217E+02 C 31738 BOND = 8314.8326 ANGLE = 22079.9893 DIHED = 32391.0503 VDWAALS = -24136.6173 EEL = -190357.8421 EGB = -63086.5533 1-4 VDW = 10733.3451 1-4 EEL = 146214.1488 RESTRAINT = 0.0000 ESURF = 987.1421 minimization completed, ENE= -.56860504E+05 RMS= 0.172286E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6617E+04 1.7341E+01 1.2899E+02 N 29129 BOND = 8416.4403 ANGLE = 22140.2890 DIHED = 32442.2861 VDWAALS = -24169.4609 EEL = -190493.7025 EGB = -62962.7930 1-4 VDW = 10763.7229 1-4 EEL = 146260.4628 RESTRAINT = 0.0000 ESURF = 986.1803 minimization completed, ENE= -.56616575E+05 RMS= 0.173405E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6418E+04 1.7335E+01 1.3609E+02 CA 18042 BOND = 8386.6449 ANGLE = 22534.0488 DIHED = 32400.1033 VDWAALS = -24035.7766 EEL = -190553.6104 EGB = -62997.9395 1-4 VDW = 10710.1128 1-4 EEL = 146147.0200 RESTRAINT = 0.0000 ESURF = 990.9671 minimization completed, ENE= -.56418429E+05 RMS= 0.173351E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6557E+04 1.7392E+01 1.3266E+02 CD 34475 BOND = 8353.4576 ANGLE = 22406.6906 DIHED = 32443.6503 VDWAALS = -24087.3006 EEL = -190888.4691 EGB = -62669.1435 1-4 VDW = 10666.3227 1-4 EEL = 146226.9586 RESTRAINT = 0.0000 ESURF = 990.5964 minimization completed, ENE= -.56557237E+05 RMS= 0.173923E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6456E+04 1.7242E+01 1.2123E+02 N 452 BOND = 8365.2516 ANGLE = 22386.4520 DIHED = 32457.6999 VDWAALS = -24007.7754 EEL = -190858.6721 EGB = -62626.9045 1-4 VDW = 10732.8322 1-4 EEL = 146098.7136 RESTRAINT = 0.0000 ESURF = 996.8323 minimization completed, ENE= -.56455570E+05 RMS= 0.172415E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6595E+04 1.7406E+01 1.2830E+02 C 737 BOND = 8463.1450 ANGLE = 22191.1973 DIHED = 32373.8959 VDWAALS = -23939.6235 EEL = -191015.7164 EGB = -62633.3755 1-4 VDW = 10716.0808 1-4 EEL = 146251.8549 RESTRAINT = 0.0000 ESURF = 997.5377 minimization completed, ENE= -.56595004E+05 RMS= 0.174059E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6561E+04 1.7386E+01 1.5349E+02 C 25761 BOND = 8543.4549 ANGLE = 22258.0621 DIHED = 32329.3201 VDWAALS = -24110.7261 EEL = -190801.8743 EGB = -62641.6420 1-4 VDW = 10692.3562 1-4 EEL = 146179.1255 RESTRAINT = 0.0000 ESURF = 990.4894 minimization completed, ENE= -.56561434E+05 RMS= 0.173857E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6547E+04 1.7296E+01 1.2509E+02 N 20512 BOND = 8345.6516 ANGLE = 22350.3283 DIHED = 32438.9424 VDWAALS = -24130.5507 EEL = -190719.2816 EGB = -62847.7983 1-4 VDW = 10701.7170 1-4 EEL = 146323.3328 RESTRAINT = 0.0000 ESURF = 991.1005 minimization completed, ENE= -.56546558E+05 RMS= 0.172964E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6538E+04 1.7368E+01 1.4558E+02 CG 35682 BOND = 8347.6979 ANGLE = 22312.2370 DIHED = 32394.1349 VDWAALS = -24144.9883 EEL = -190640.4627 EGB = -62888.0844 1-4 VDW = 10693.9522 1-4 EEL = 146397.5971 RESTRAINT = 0.0000 ESURF = 989.9855 minimization completed, ENE= -.56537931E+05 RMS= 0.173681E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6928E+04 1.7201E+01 1.3376E+02 C 44514 BOND = 8279.8951 ANGLE = 22230.7458 DIHED = 32391.2161 VDWAALS = -24351.6491 EEL = -190288.6110 EGB = -63081.7977 1-4 VDW = 10717.7903 1-4 EEL = 146182.9158 RESTRAINT = 0.0000 ESURF = 991.0915 minimization completed, ENE= -.56928403E+05 RMS= 0.172011E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6394E+04 1.7384E+01 1.2830E+02 C 33817 BOND = 8474.9702 ANGLE = 22316.7466 DIHED = 32439.3587 VDWAALS = -24098.1942 EEL = -190279.7409 EGB = -63291.8772 1-4 VDW = 10726.3579 1-4 EEL = 146327.7543 RESTRAINT = 0.0000 ESURF = 990.3623 minimization completed, ENE= -.56394262E+05 RMS= 0.173842E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6618E+04 1.7345E+01 1.2017E+02 C 41153 BOND = 8353.4477 ANGLE = 22200.2427 DIHED = 32419.2636 VDWAALS = -24121.9859 EEL = -190683.0106 EGB = -63020.2990 1-4 VDW = 10810.3614 1-4 EEL = 146434.5409 RESTRAINT = 0.0000 ESURF = 989.3905 minimization completed, ENE= -.56618049E+05 RMS= 0.173446E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6549E+04 1.7326E+01 1.2963E+02 CG 30040 BOND = 8468.6017 ANGLE = 22284.8208 DIHED = 32433.2022 VDWAALS = -24218.2255 EEL = -190164.1779 EGB = -63186.6344 1-4 VDW = 10660.6419 1-4 EEL = 146181.6404 RESTRAINT = 0.0000 ESURF = 990.8301 minimization completed, ENE= -.56549301E+05 RMS= 0.173264E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6508E+04 1.7367E+01 1.2443E+02 C 9577 BOND = 8476.1657 ANGLE = 22215.1249 DIHED = 32447.2740 VDWAALS = -24278.4452 EEL = -190367.6875 EGB = -62864.6772 1-4 VDW = 10772.3378 1-4 EEL = 146108.1194 RESTRAINT = 0.0000 ESURF = 984.0903 minimization completed, ENE= -.56507698E+05 RMS= 0.173670E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6616E+04 1.7291E+01 1.2754E+02 C 11545 BOND = 8404.2550 ANGLE = 22111.5362 DIHED = 32435.7382 VDWAALS = -24003.9098 EEL = -190400.3527 EGB = -63083.6064 1-4 VDW = 10731.2504 1-4 EEL = 146198.3454 RESTRAINT = 0.0000 ESURF = 990.8109 minimization completed, ENE= -.56615933E+05 RMS= 0.172911E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6138E+04 1.7410E+01 1.5832E+02 C 34401 BOND = 8466.8157 ANGLE = 22439.0921 DIHED = 32491.7594 VDWAALS = -23986.1790 EEL = -190579.0978 EGB = -63013.5313 1-4 VDW = 10731.7599 1-4 EEL = 146323.1206 RESTRAINT = 0.0000 ESURF = 988.6077 minimization completed, ENE= -.56137653E+05 RMS= 0.174097E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6617E+04 1.7291E+01 1.2299E+02 CD 37308 BOND = 8351.9175 ANGLE = 22216.6565 DIHED = 32368.4233 VDWAALS = -24048.2827 EEL = -190267.3857 EGB = -63167.3833 1-4 VDW = 10720.0430 1-4 EEL = 146219.5349 RESTRAINT = 0.0000 ESURF = 989.6261 minimization completed, ENE= -.56616850E+05 RMS= 0.172909E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2841.08 ( 4.91% of Gen B) | Calc gb diag 13611.48 (23.53% of Gen B) | Calc gb off-diag 41395.74 (71.56% of Gen B) | Gen Born time 57848.32 (100.0% of Nonbo) | Nonbond force 57848.32 (100.0% of Force) | Bond/Angle/Dihedral 17.84 ( 0.03% of Force) | Force time 57866.19 (100.0% of Runmd) | Runmd Time 57866.19 (99.84% of Total) | Other 90.23 ( 0.16% of Total) | Total time 57956.56 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:33:40.528 on 10/17/2010 | Setup done at 07:33:44.700 on 10/17/2010 | Run done at 23:39:37.084 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:33:34 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.24 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.24 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6401E+04 1.7430E+01 1.3731E+02 CG 30367 BOND = 8503.0183 ANGLE = 22323.5129 DIHED = 32438.0292 VDWAALS = -24069.5496 EEL = -190635.5255 EGB = -62844.1676 1-4 VDW = 10726.7694 1-4 EEL = 146161.3256 RESTRAINT = 0.0000 ESURF = 995.9307 minimization completed, ENE= -.56400656E+05 RMS= 0.174297E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6472E+04 1.7224E+01 1.3082E+02 C 27705 BOND = 8501.1322 ANGLE = 22228.2115 DIHED = 32441.6511 VDWAALS = -24051.8627 EEL = -190689.0767 EGB = -62523.5956 1-4 VDW = 10671.9256 1-4 EEL = 145956.9331 RESTRAINT = 0.0000 ESURF = 992.8801 minimization completed, ENE= -.56471801E+05 RMS= 0.172242E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6420E+04 1.7296E+01 1.1248E+02 N 24513 BOND = 8386.8773 ANGLE = 22435.5829 DIHED = 32443.4843 VDWAALS = -24163.6030 EEL = -190576.1618 EGB = -62840.1868 1-4 VDW = 10720.8591 1-4 EEL = 146181.6348 RESTRAINT = 0.0000 ESURF = 991.2114 minimization completed, ENE= -.56420302E+05 RMS= 0.172961E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6487E+04 1.7327E+01 1.1875E+02 C 38955 BOND = 8485.3758 ANGLE = 22294.5335 DIHED = 32483.0290 VDWAALS = -24234.1663 EEL = -190728.9268 EGB = -62555.0116 1-4 VDW = 10686.0098 1-4 EEL = 146090.2052 RESTRAINT = 0.0000 ESURF = 992.0725 minimization completed, ENE= -.56486879E+05 RMS= 0.173270E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6598E+04 1.7308E+01 1.3487E+02 C 46397 BOND = 8461.1808 ANGLE = 22213.6740 DIHED = 32394.7574 VDWAALS = -23981.8449 EEL = -191041.5225 EGB = -62521.9806 1-4 VDW = 10732.3505 1-4 EEL = 146154.7127 RESTRAINT = 0.0000 ESURF = 990.2226 minimization completed, ENE= -.56598450E+05 RMS= 0.173084E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6569E+04 1.7192E+01 1.4840E+02 C 15450 BOND = 8240.2451 ANGLE = 22417.0741 DIHED = 32391.9240 VDWAALS = -24087.3232 EEL = -190920.2501 EGB = -62556.5433 1-4 VDW = 10719.5372 1-4 EEL = 146236.7443 RESTRAINT = 0.0000 ESURF = 989.3792 minimization completed, ENE= -.56569213E+05 RMS= 0.171923E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6521E+04 1.7304E+01 1.4603E+02 C 41431 BOND = 8242.3795 ANGLE = 22445.3437 DIHED = 32483.0687 VDWAALS = -24115.6298 EEL = -191262.0872 EGB = -62267.3219 1-4 VDW = 10775.4620 1-4 EEL = 146186.3657 RESTRAINT = 0.0000 ESURF = 991.4905 minimization completed, ENE= -.56520929E+05 RMS= 0.173044E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6433E+04 1.7338E+01 1.2760E+02 C 45168 BOND = 8377.9060 ANGLE = 22462.5175 DIHED = 32425.6635 VDWAALS = -24118.9922 EEL = -191049.5578 EGB = -62557.4333 1-4 VDW = 10708.5566 1-4 EEL = 146326.1274 RESTRAINT = 0.0000 ESURF = 991.9177 minimization completed, ENE= -.56433295E+05 RMS= 0.173376E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6421E+04 1.7298E+01 1.3911E+02 CZ 45245 BOND = 8385.0100 ANGLE = 22272.2944 DIHED = 32449.3844 VDWAALS = -24208.7186 EEL = -190510.3721 EGB = -62698.3468 1-4 VDW = 10765.6545 1-4 EEL = 146128.9378 RESTRAINT = 0.0000 ESURF = 995.5543 minimization completed, ENE= -.56420602E+05 RMS= 0.172984E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6680E+04 1.7248E+01 1.2791E+02 C 42814 BOND = 8403.6250 ANGLE = 22265.6731 DIHED = 32338.9745 VDWAALS = -24030.6847 EEL = -190871.9594 EGB = -62613.7182 1-4 VDW = 10708.8882 1-4 EEL = 146127.8362 RESTRAINT = 0.0000 ESURF = 991.0162 minimization completed, ENE= -.56680349E+05 RMS= 0.172479E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6340E+04 1.7340E+01 1.3345E+02 C 31486 BOND = 8440.9326 ANGLE = 22214.0982 DIHED = 32522.8965 VDWAALS = -23958.6024 EEL = -191008.3882 EGB = -62577.2114 1-4 VDW = 10792.6444 1-4 EEL = 146237.2975 RESTRAINT = 0.0000 ESURF = 995.8656 minimization completed, ENE= -.56340467E+05 RMS= 0.173401E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6576E+04 1.7250E+01 1.1993E+02 C 40583 BOND = 8278.2495 ANGLE = 22239.2067 DIHED = 32404.3554 VDWAALS = -24101.0614 EEL = -191026.3098 EGB = -62400.4574 1-4 VDW = 10804.6338 1-4 EEL = 146235.8795 RESTRAINT = 0.0000 ESURF = 989.3327 minimization completed, ENE= -.56576171E+05 RMS= 0.172504E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6669E+04 1.7375E+01 1.1712E+02 CA 35336 BOND = 8473.7175 ANGLE = 22203.1997 DIHED = 32389.8709 VDWAALS = -24226.1095 EEL = -190456.9101 EGB = -62833.2058 1-4 VDW = 10670.3449 1-4 EEL = 146117.1971 RESTRAINT = 0.0000 ESURF = 992.4915 minimization completed, ENE= -.56669404E+05 RMS= 0.173754E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6568E+04 1.7377E+01 1.5391E+02 C 41696 BOND = 8371.0961 ANGLE = 22276.7779 DIHED = 32351.1803 VDWAALS = -24198.4065 EEL = -190486.5580 EGB = -62885.5926 1-4 VDW = 10737.0934 1-4 EEL = 146273.6220 RESTRAINT = 0.0000 ESURF = 993.0034 minimization completed, ENE= -.56567784E+05 RMS= 0.173773E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6605E+04 1.7312E+01 1.2737E+02 CZ 5139 BOND = 8375.5914 ANGLE = 22327.8185 DIHED = 32349.8994 VDWAALS = -24176.5403 EEL = -190507.0552 EGB = -63042.1925 1-4 VDW = 10801.9356 1-4 EEL = 146274.6528 RESTRAINT = 0.0000 ESURF = 990.6140 minimization completed, ENE= -.56605276E+05 RMS= 0.173117E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6554E+04 1.7391E+01 1.4160E+02 C 40943 BOND = 8365.1912 ANGLE = 22352.5606 DIHED = 32437.3483 VDWAALS = -24077.4494 EEL = -191063.1402 EGB = -62552.6920 1-4 VDW = 10730.4884 1-4 EEL = 146266.8059 RESTRAINT = 0.0000 ESURF = 987.1406 minimization completed, ENE= -.56553747E+05 RMS= 0.173913E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6530E+04 1.7428E+01 1.3653E+02 C 40044 BOND = 8507.3071 ANGLE = 22351.5456 DIHED = 32393.8605 VDWAALS = -24067.3807 EEL = -190678.1951 EGB = -62763.8536 1-4 VDW = 10618.3327 1-4 EEL = 146113.6451 RESTRAINT = 0.0000 ESURF = 994.8054 minimization completed, ENE= -.56529933E+05 RMS= 0.174283E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6517E+04 1.7365E+01 1.3371E+02 CG 4342 BOND = 8435.5545 ANGLE = 22226.4734 DIHED = 32449.9852 VDWAALS = -24105.4131 EEL = -191016.5767 EGB = -62491.1641 1-4 VDW = 10747.6280 1-4 EEL = 146244.3128 RESTRAINT = 0.0000 ESURF = 992.2794 minimization completed, ENE= -.56516921E+05 RMS= 0.173651E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6666E+04 1.7322E+01 1.3847E+02 C 43445 BOND = 8429.8409 ANGLE = 22198.0667 DIHED = 32377.6464 VDWAALS = -24067.6033 EEL = -190628.9074 EGB = -62829.9145 1-4 VDW = 10746.7721 1-4 EEL = 146116.3153 RESTRAINT = 0.0000 ESURF = 991.6598 minimization completed, ENE= -.56666124E+05 RMS= 0.173224E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6545E+04 1.7356E+01 1.2750E+02 CG 29485 BOND = 8412.8414 ANGLE = 22380.0395 DIHED = 32467.0006 VDWAALS = -24113.1881 EEL = -190800.6231 EGB = -62612.3269 1-4 VDW = 10692.4785 1-4 EEL = 146038.3102 RESTRAINT = 0.0000 ESURF = 990.8512 minimization completed, ENE= -.56544617E+05 RMS= 0.173564E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6571E+04 1.7369E+01 1.3564E+02 C 39783 BOND = 8521.3048 ANGLE = 22245.3691 DIHED = 32377.7435 VDWAALS = -24061.2343 EEL = -190343.7886 EGB = -63043.1428 1-4 VDW = 10699.3403 1-4 EEL = 146043.5764 RESTRAINT = 0.0000 ESURF = 990.1887 minimization completed, ENE= -.56570643E+05 RMS= 0.173687E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6433E+04 1.7424E+01 1.2894E+02 CA 17704 BOND = 8465.9516 ANGLE = 22416.7456 DIHED = 32362.9289 VDWAALS = -24200.7028 EEL = -190575.1908 EGB = -62855.6574 1-4 VDW = 10713.1925 1-4 EEL = 146247.8435 RESTRAINT = 0.0000 ESURF = 992.1129 minimization completed, ENE= -.56432776E+05 RMS= 0.174235E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6407E+04 1.7403E+01 1.2599E+02 C 45228 BOND = 8491.5278 ANGLE = 22350.0970 DIHED = 32363.3044 VDWAALS = -24121.5592 EEL = -190733.8280 EGB = -62700.3839 1-4 VDW = 10773.3478 1-4 EEL = 146188.5370 RESTRAINT = 0.0000 ESURF = 981.7914 minimization completed, ENE= -.56407166E+05 RMS= 0.174031E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6488E+04 1.7335E+01 1.2482E+02 CA 12390 BOND = 8398.6956 ANGLE = 22239.8618 DIHED = 32406.1684 VDWAALS = -24126.2234 EEL = -190633.9760 EGB = -62836.1500 1-4 VDW = 10726.8896 1-4 EEL = 146349.6813 RESTRAINT = 0.0000 ESURF = 987.3728 minimization completed, ENE= -.56487680E+05 RMS= 0.173355E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6624E+04 1.7449E+01 1.1862E+02 C 8787 BOND = 8460.0274 ANGLE = 22153.1382 DIHED = 32407.4629 VDWAALS = -24048.8173 EEL = -190330.6302 EGB = -63256.7424 1-4 VDW = 10741.1777 1-4 EEL = 146257.5845 RESTRAINT = 0.0000 ESURF = 992.3868 minimization completed, ENE= -.56624413E+05 RMS= 0.174493E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2868.65 ( 4.98% of Gen B) | Calc gb diag 13690.06 (23.77% of Gen B) | Calc gb off-diag 41027.70 (71.25% of Gen B) | Gen Born time 57586.42 (100.0% of Nonbo) | Nonbond force 57586.42 (100.0% of Force) | Bond/Angle/Dihedral 15.09 ( 0.03% of Force) | Force time 57601.54 (100.0% of Runmd) | Runmd Time 57601.54 (99.84% of Total) | Other 92.01 ( 0.16% of Total) | Total time 57693.68 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:33:34.339 on 10/17/2010 | Setup done at 07:33:37.584 on 10/17/2010 | Run done at 23:35:08.024 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:33:27 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.23 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.23 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6797E+04 1.7297E+01 1.2867E+02 N 3027 BOND = 8395.1193 ANGLE = 22132.7678 DIHED = 32257.4777 VDWAALS = -24151.9468 EEL = -190939.9006 EGB = -62313.1176 1-4 VDW = 10687.8426 1-4 EEL = 146147.0948 RESTRAINT = 0.0000 ESURF = 987.9994 minimization completed, ENE= -.56796663E+05 RMS= 0.172969E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6618E+04 1.7416E+01 1.2284E+02 C 23503 BOND = 8451.7346 ANGLE = 22259.9722 DIHED = 32369.2972 VDWAALS = -24188.3774 EEL = -190506.1521 EGB = -62606.1712 1-4 VDW = 10644.9345 1-4 EEL = 145966.5816 RESTRAINT = 0.0000 ESURF = 989.8925 minimization completed, ENE= -.56618288E+05 RMS= 0.174155E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6555E+04 1.7298E+01 1.2688E+02 C 10165 BOND = 8387.1929 ANGLE = 21992.3693 DIHED = 32518.8557 VDWAALS = -24179.8169 EEL = -190363.3560 EGB = -62892.7985 1-4 VDW = 10751.7874 1-4 EEL = 146242.9814 RESTRAINT = 0.0000 ESURF = 987.4049 minimization completed, ENE= -.56555380E+05 RMS= 0.172977E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6272E+04 1.7382E+01 1.3006E+02 C 18662 BOND = 8527.0494 ANGLE = 22312.7865 DIHED = 32465.6491 VDWAALS = -24113.8089 EEL = -190111.6204 EGB = -63089.6030 1-4 VDW = 10713.0028 1-4 EEL = 146033.2622 RESTRAINT = 0.0000 ESURF = 991.5938 minimization completed, ENE= -.56271689E+05 RMS= 0.173821E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6494E+04 1.7290E+01 1.4670E+02 C 1156 BOND = 8294.3085 ANGLE = 22244.1099 DIHED = 32518.2694 VDWAALS = -24082.7408 EEL = -190734.7330 EGB = -62656.2902 1-4 VDW = 10773.9523 1-4 EEL = 146160.4357 RESTRAINT = 0.0000 ESURF = 988.9252 minimization completed, ENE= -.56493763E+05 RMS= 0.172900E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6820E+04 1.7238E+01 1.2650E+02 C 34401 BOND = 8263.8515 ANGLE = 22081.5083 DIHED = 32389.6337 VDWAALS = -24149.3776 EEL = -190326.9768 EGB = -62850.2421 1-4 VDW = 10682.2669 1-4 EEL = 146103.1303 RESTRAINT = 0.0000 ESURF = 985.7165 minimization completed, ENE= -.56820489E+05 RMS= 0.172375E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6248E+04 1.7463E+01 1.3053E+02 CZ 35581 BOND = 8419.8232 ANGLE = 22397.4907 DIHED = 32441.7353 VDWAALS = -24143.2173 EEL = -190570.3051 EGB = -62675.5492 1-4 VDW = 10753.7947 1-4 EEL = 146145.4053 RESTRAINT = 0.0000 ESURF = 982.9560 minimization completed, ENE= -.56247866E+05 RMS= 0.174633E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6689E+04 1.7303E+01 1.2782E+02 C 25873 BOND = 8412.0066 ANGLE = 22247.3090 DIHED = 32537.7082 VDWAALS = -24176.9986 EEL = -190481.4545 EGB = -62924.5281 1-4 VDW = 10626.1341 1-4 EEL = 146087.2451 RESTRAINT = 0.0000 ESURF = 983.4570 minimization completed, ENE= -.56689121E+05 RMS= 0.173030E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6503E+04 1.7308E+01 1.3037E+02 CZ 46736 BOND = 8397.9284 ANGLE = 22289.9855 DIHED = 32412.8945 VDWAALS = -24213.9356 EEL = -190432.1470 EGB = -62826.6366 1-4 VDW = 10758.0250 1-4 EEL = 146126.0940 RESTRAINT = 0.0000 ESURF = 984.4934 minimization completed, ENE= -.56503298E+05 RMS= 0.173075E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6821E+04 1.7269E+01 1.5242E+02 C 31655 BOND = 8228.0556 ANGLE = 22114.6076 DIHED = 32475.9833 VDWAALS = -24159.7743 EEL = -190549.1671 EGB = -62737.8168 1-4 VDW = 10707.7174 1-4 EEL = 146114.7134 RESTRAINT = 0.0000 ESURF = 984.6758 minimization completed, ENE= -.56821005E+05 RMS= 0.172688E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6421E+04 1.7264E+01 1.4865E+02 CD 41065 BOND = 8356.8317 ANGLE = 22322.3865 DIHED = 32500.1431 VDWAALS = -24075.0500 EEL = -191100.4922 EGB = -62417.0894 1-4 VDW = 10798.0158 1-4 EEL = 146205.6825 RESTRAINT = 0.0000 ESURF = 989.0638 minimization completed, ENE= -.56420508E+05 RMS= 0.172640E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6567E+04 1.7354E+01 1.3430E+02 CD 12945 BOND = 8398.1944 ANGLE = 22237.0698 DIHED = 32453.1089 VDWAALS = -24181.4912 EEL = -190553.7893 EGB = -62770.0347 1-4 VDW = 10689.9713 1-4 EEL = 146178.7577 RESTRAINT = 0.0000 ESURF = 981.4969 minimization completed, ENE= -.56566716E+05 RMS= 0.173539E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6424E+04 1.7336E+01 1.2844E+02 C 16722 BOND = 8412.1898 ANGLE = 22315.4917 DIHED = 32614.8826 VDWAALS = -24176.7805 EEL = -190537.2817 EGB = -62891.7908 1-4 VDW = 10702.3751 1-4 EEL = 146150.3766 RESTRAINT = 0.0000 ESURF = 986.3385 minimization completed, ENE= -.56424199E+05 RMS= 0.173360E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6580E+04 1.7373E+01 1.4271E+02 C 36261 BOND = 8372.6791 ANGLE = 22191.7455 DIHED = 32531.1365 VDWAALS = -24200.5710 EEL = -190466.7510 EGB = -62699.5471 1-4 VDW = 10655.7166 1-4 EEL = 146049.0178 RESTRAINT = 0.0000 ESURF = 986.6776 minimization completed, ENE= -.56579896E+05 RMS= 0.173730E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6681E+04 1.7252E+01 1.3942E+02 CD 29999 BOND = 8262.4836 ANGLE = 22280.8009 DIHED = 32311.0111 VDWAALS = -24023.1514 EEL = -191028.4929 EGB = -62380.7119 1-4 VDW = 10816.5558 1-4 EEL = 146091.9206 RESTRAINT = 0.0000 ESURF = 989.0337 minimization completed, ENE= -.56680550E+05 RMS= 0.172515E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6380E+04 1.7323E+01 1.2109E+02 C 642 BOND = 8381.8628 ANGLE = 22478.6938 DIHED = 32400.3905 VDWAALS = -24171.8161 EEL = -190780.5179 EGB = -62504.9121 1-4 VDW = 10727.0742 1-4 EEL = 146098.8394 RESTRAINT = 0.0000 ESURF = 989.9467 minimization completed, ENE= -.56380439E+05 RMS= 0.173228E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6424E+04 1.7302E+01 1.5596E+02 C 34743 BOND = 8347.8475 ANGLE = 22200.1704 DIHED = 32485.0847 VDWAALS = -24229.3132 EEL = -190414.1623 EGB = -62719.4571 1-4 VDW = 10820.7854 1-4 EEL = 146097.4197 RESTRAINT = 0.0000 ESURF = 987.2141 minimization completed, ENE= -.56424411E+05 RMS= 0.173016E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6272E+04 1.7359E+01 1.2603E+02 CD 33730 BOND = 8425.3071 ANGLE = 22441.9857 DIHED = 32455.9201 VDWAALS = -24244.1768 EEL = -190416.1800 EGB = -62890.2213 1-4 VDW = 10758.3143 1-4 EEL = 146203.6363 RESTRAINT = 0.0000 ESURF = 993.3220 minimization completed, ENE= -.56272093E+05 RMS= 0.173588E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6389E+04 1.7474E+01 1.5241E+02 C 26801 BOND = 8547.3881 ANGLE = 22367.0133 DIHED = 32431.5828 VDWAALS = -24096.1361 EEL = -190200.3739 EGB = -63124.0020 1-4 VDW = 10668.1683 1-4 EEL = 146028.0958 RESTRAINT = 0.0000 ESURF = 989.1900 minimization completed, ENE= -.56389074E+05 RMS= 0.174739E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6582E+04 1.7426E+01 1.3147E+02 N 33841 BOND = 8432.4280 ANGLE = 22237.8970 DIHED = 32417.7951 VDWAALS = -24104.5028 EEL = -191201.7038 EGB = -62494.7006 1-4 VDW = 10768.0545 1-4 EEL = 146372.4598 RESTRAINT = 0.0000 ESURF = 990.0452 minimization completed, ENE= -.56582228E+05 RMS= 0.174257E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6524E+04 1.7366E+01 1.2487E+02 C 22892 BOND = 8477.4456 ANGLE = 22127.8723 DIHED = 32482.5902 VDWAALS = -24052.9170 EEL = -190699.8410 EGB = -62739.6187 1-4 VDW = 10692.6013 1-4 EEL = 146196.6729 RESTRAINT = 0.0000 ESURF = 991.1818 minimization completed, ENE= -.56524013E+05 RMS= 0.173663E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6492E+04 1.7454E+01 1.4922E+02 C 39114 BOND = 8340.5885 ANGLE = 22289.5486 DIHED = 32415.9833 VDWAALS = -23982.3247 EEL = -190480.6414 EGB = -62936.5435 1-4 VDW = 10705.8432 1-4 EEL = 146157.8348 RESTRAINT = 0.0000 ESURF = 997.2344 minimization completed, ENE= -.56492477E+05 RMS= 0.174536E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6673E+04 1.7337E+01 1.3377E+02 CG 18690 BOND = 8428.4884 ANGLE = 22093.0932 DIHED = 32451.0075 VDWAALS = -24061.9007 EEL = -190902.4038 EGB = -62483.1611 1-4 VDW = 10694.2017 1-4 EEL = 146114.2579 RESTRAINT = 0.0000 ESURF = 993.8178 minimization completed, ENE= -.56672599E+05 RMS= 0.173375E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6021E+04 1.7369E+01 1.3878E+02 C 21 BOND = 8430.7805 ANGLE = 22544.1333 DIHED = 32536.1896 VDWAALS = -24068.2356 EEL = -190737.1871 EGB = -62615.6835 1-4 VDW = 10764.3753 1-4 EEL = 146135.1640 RESTRAINT = 0.0000 ESURF = 989.0772 minimization completed, ENE= -.56021386E+05 RMS= 0.173688E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6305E+04 1.7449E+01 1.3268E+02 C 31496 BOND = 8494.8298 ANGLE = 22456.4305 DIHED = 32522.1304 VDWAALS = -24051.4756 EEL = -190569.1696 EGB = -62932.6786 1-4 VDW = 10710.2950 1-4 EEL = 146073.0416 RESTRAINT = 0.0000 ESURF = 991.9422 minimization completed, ENE= -.56304654E+05 RMS= 0.174485E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2857.75 ( 4.97% of Gen B) | Calc gb diag 13866.60 (24.11% of Gen B) | Calc gb off-diag 40779.34 (70.92% of Gen B) | Gen Born time 57503.70 (100.0% of Nonbo) | Nonbond force 57503.70 (100.0% of Force) | Bond/Angle/Dihedral 16.58 ( 0.03% of Force) | Force time 57520.31 (100.0% of Runmd) | Runmd Time 57520.31 (99.86% of Total) | Other 82.28 ( 0.14% of Total) | Total time 57602.72 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:33:27.652 on 10/17/2010 | Setup done at 07:33:30.884 on 10/17/2010 | Run done at 23:33:30.374 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:33:21 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.22 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.22 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6511E+04 1.7287E+01 1.3218E+02 NH2 36483 BOND = 8260.8746 ANGLE = 22411.6833 DIHED = 32464.1813 VDWAALS = -24160.5848 EEL = -190532.6852 EGB = -62759.6929 1-4 VDW = 10713.0937 1-4 EEL = 146101.9498 RESTRAINT = 0.0000 ESURF = 990.4971 minimization completed, ENE= -.56510683E+05 RMS= 0.172870E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6382E+04 1.7362E+01 1.2577E+02 C 6497 BOND = 8500.4456 ANGLE = 22339.0781 DIHED = 32388.1165 VDWAALS = -24165.5006 EEL = -190627.3063 EGB = -62723.2574 1-4 VDW = 10751.0323 1-4 EEL = 146167.4395 RESTRAINT = 0.0000 ESURF = 987.7594 minimization completed, ENE= -.56382193E+05 RMS= 0.173624E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6559E+04 1.7291E+01 1.2021E+02 C 8285 BOND = 8459.5657 ANGLE = 22270.1358 DIHED = 32404.0145 VDWAALS = -24055.7460 EEL = -190387.9363 EGB = -63004.6075 1-4 VDW = 10652.7003 1-4 EEL = 146113.6735 RESTRAINT = 0.0000 ESURF = 988.7334 minimization completed, ENE= -.56559467E+05 RMS= 0.172906E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6805E+04 1.7271E+01 1.3968E+02 C 11262 BOND = 8366.0314 ANGLE = 22116.7919 DIHED = 32393.0535 VDWAALS = -24151.9480 EEL = -190320.5435 EGB = -63032.6980 1-4 VDW = 10661.0468 1-4 EEL = 146171.2757 RESTRAINT = 0.0000 ESURF = 991.7364 minimization completed, ENE= -.56805254E+05 RMS= 0.172715E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6817E+04 1.7231E+01 1.4674E+02 C 3183 BOND = 8222.6668 ANGLE = 22122.0539 DIHED = 32399.4197 VDWAALS = -24130.6927 EEL = -191024.7422 EGB = -62344.8097 1-4 VDW = 10740.4798 1-4 EEL = 146214.3719 RESTRAINT = 0.0000 ESURF = 984.5961 minimization completed, ENE= -.56816656E+05 RMS= 0.172315E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6485E+04 1.7343E+01 1.4215E+02 CG 17344 BOND = 8434.1614 ANGLE = 22515.3897 DIHED = 32328.7468 VDWAALS = -24089.4035 EEL = -190770.2595 EGB = -62668.2027 1-4 VDW = 10686.8754 1-4 EEL = 146089.1297 RESTRAINT = 0.0000 ESURF = 988.2303 minimization completed, ENE= -.56485332E+05 RMS= 0.173426E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6533E+04 1.7373E+01 1.3135E+02 CG 369 BOND = 8395.6274 ANGLE = 22271.3457 DIHED = 32436.3157 VDWAALS = -24160.1880 EEL = -191336.0569 EGB = -62213.3121 1-4 VDW = 10716.2023 1-4 EEL = 146372.3160 RESTRAINT = 0.0000 ESURF = 985.2298 minimization completed, ENE= -.56532520E+05 RMS= 0.173733E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6651E+04 1.7403E+01 1.2725E+02 C 22970 BOND = 8438.9894 ANGLE = 22132.9977 DIHED = 32487.3701 VDWAALS = -24188.8714 EEL = -190532.9555 EGB = -62764.9624 1-4 VDW = 10709.7183 1-4 EEL = 146081.3339 RESTRAINT = 0.0000 ESURF = 985.6634 minimization completed, ENE= -.56650716E+05 RMS= 0.174033E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6862E+04 1.7281E+01 1.3087E+02 C 20214 BOND = 8356.3165 ANGLE = 22227.5920 DIHED = 32369.1359 VDWAALS = -24229.0843 EEL = -190964.6260 EGB = -62450.6725 1-4 VDW = 10688.2238 1-4 EEL = 146153.5912 RESTRAINT = 0.0000 ESURF = 987.8746 minimization completed, ENE= -.56861649E+05 RMS= 0.172812E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6536E+04 1.7360E+01 1.2112E+02 CG 37738 BOND = 8465.1339 ANGLE = 22364.6847 DIHED = 32395.2046 VDWAALS = -24194.6325 EEL = -191309.8276 EGB = -62289.2100 1-4 VDW = 10706.0975 1-4 EEL = 146338.0378 RESTRAINT = 0.0000 ESURF = 988.0753 minimization completed, ENE= -.56536436E+05 RMS= 0.173597E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6505E+04 1.7344E+01 1.3172E+02 C 12437 BOND = 8421.0746 ANGLE = 22213.2563 DIHED = 32464.3092 VDWAALS = -24131.6231 EEL = -190979.0306 EGB = -62447.9332 1-4 VDW = 10810.4183 1-4 EEL = 146153.4780 RESTRAINT = 0.0000 ESURF = 991.1451 minimization completed, ENE= -.56504905E+05 RMS= 0.173437E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6561E+04 1.7323E+01 1.2053E+02 N 18579 BOND = 8292.5919 ANGLE = 22374.1866 DIHED = 32432.3961 VDWAALS = -24219.8654 EEL = -190677.2554 EGB = -62571.2516 1-4 VDW = 10720.2266 1-4 EEL = 146099.6060 RESTRAINT = 0.0000 ESURF = 988.0425 minimization completed, ENE= -.56561323E+05 RMS= 0.173232E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6627E+04 1.7427E+01 1.2589E+02 C 44174 BOND = 8462.7533 ANGLE = 22237.8082 DIHED = 32472.6965 VDWAALS = -24245.4873 EEL = -190518.2372 EGB = -62797.6630 1-4 VDW = 10732.5333 1-4 EEL = 146039.1473 RESTRAINT = 0.0000 ESURF = 988.9596 minimization completed, ENE= -.56627489E+05 RMS= 0.174267E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6433E+04 1.7319E+01 1.3846E+02 CG 1248 BOND = 8315.0781 ANGLE = 22390.2143 DIHED = 32406.2570 VDWAALS = -24081.6236 EEL = -191048.7126 EGB = -62374.6243 1-4 VDW = 10791.9490 1-4 EEL = 146176.6103 RESTRAINT = 0.0000 ESURF = 991.5027 minimization completed, ENE= -.56433349E+05 RMS= 0.173185E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6698E+04 1.7361E+01 1.2293E+02 C 10807 BOND = 8396.6338 ANGLE = 22306.4338 DIHED = 32351.9598 VDWAALS = -24182.9389 EEL = -190907.3548 EGB = -62460.9855 1-4 VDW = 10691.4919 1-4 EEL = 146120.7275 RESTRAINT = 0.0000 ESURF = 985.9547 minimization completed, ENE= -.56698078E+05 RMS= 0.173607E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6456E+04 1.7316E+01 1.3183E+02 C 17766 BOND = 8372.7413 ANGLE = 22384.5722 DIHED = 32409.1130 VDWAALS = -24146.4346 EEL = -190755.3583 EGB = -62536.3074 1-4 VDW = 10682.6294 1-4 EEL = 146146.6277 RESTRAINT = 0.0000 ESURF = 986.3816 minimization completed, ENE= -.56456035E+05 RMS= 0.173163E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6547E+04 1.7312E+01 1.0696E+02 C 36247 BOND = 8323.2278 ANGLE = 22248.7047 DIHED = 32492.8405 VDWAALS = -24103.6469 EEL = -191117.9966 EGB = -62340.6896 1-4 VDW = 10703.8707 1-4 EEL = 146261.5061 RESTRAINT = 0.0000 ESURF = 984.8500 minimization completed, ENE= -.56547333E+05 RMS= 0.173121E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6608E+04 1.7216E+01 1.3473E+02 C 19129 BOND = 8265.0503 ANGLE = 22235.7510 DIHED = 32326.8867 VDWAALS = -24143.0755 EEL = -191002.3667 EGB = -62413.2762 1-4 VDW = 10798.0217 1-4 EEL = 146340.3813 RESTRAINT = 0.0000 ESURF = 984.7869 minimization completed, ENE= -.56607841E+05 RMS= 0.172159E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6690E+04 1.7285E+01 1.4885E+02 C 36832 BOND = 8238.7640 ANGLE = 22214.5888 DIHED = 32460.4704 VDWAALS = -24088.7115 EEL = -190974.5394 EGB = -62476.5058 1-4 VDW = 10704.4923 1-4 EEL = 146243.3318 RESTRAINT = 0.0000 ESURF = 987.7399 minimization completed, ENE= -.56690370E+05 RMS= 0.172847E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6550E+04 1.7266E+01 1.4324E+02 C 23576 BOND = 8354.4292 ANGLE = 22209.7832 DIHED = 32445.9808 VDWAALS = -24091.2374 EEL = -191199.3003 EGB = -62316.8844 1-4 VDW = 10769.2587 1-4 EEL = 146289.0599 RESTRAINT = 0.0000 ESURF = 989.2472 minimization completed, ENE= -.56549663E+05 RMS= 0.172661E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6482E+04 1.7393E+01 1.3479E+02 C 35673 BOND = 8552.0309 ANGLE = 22193.6127 DIHED = 32381.8723 VDWAALS = -24071.3067 EEL = -191023.7837 EGB = -62276.3604 1-4 VDW = 10704.3763 1-4 EEL = 146071.2832 RESTRAINT = 0.0000 ESURF = 986.6984 minimization completed, ENE= -.56481577E+05 RMS= 0.173925E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6436E+04 1.7361E+01 1.3887E+02 C 42545 BOND = 8531.0637 ANGLE = 22259.7700 DIHED = 32441.7631 VDWAALS = -24207.2426 EEL = -190626.3398 EGB = -62567.9622 1-4 VDW = 10670.3515 1-4 EEL = 146076.1377 RESTRAINT = 0.0000 ESURF = 986.3788 minimization completed, ENE= -.56436080E+05 RMS= 0.173609E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6596E+04 1.7381E+01 1.4872E+02 C 35012 BOND = 8491.8243 ANGLE = 21998.1603 DIHED = 32482.5475 VDWAALS = -24134.4616 EEL = -190573.3561 EGB = -62705.0661 1-4 VDW = 10694.3231 1-4 EEL = 146164.5562 RESTRAINT = 0.0000 ESURF = 985.1335 minimization completed, ENE= -.56596339E+05 RMS= 0.173815E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6827E+04 1.7271E+01 1.2963E+02 CG 39227 BOND = 8473.2474 ANGLE = 22081.9256 DIHED = 32366.8300 VDWAALS = -24101.4141 EEL = -190935.0141 EGB = -62546.4331 1-4 VDW = 10634.4257 1-4 EEL = 146213.6745 RESTRAINT = 0.0000 ESURF = 985.8012 minimization completed, ENE= -.56826957E+05 RMS= 0.172705E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6602E+04 1.7302E+01 1.3015E+02 C 40917 BOND = 8390.8021 ANGLE = 22260.0472 DIHED = 32451.3671 VDWAALS = -24078.4195 EEL = -191276.3728 EGB = -62400.8656 1-4 VDW = 10759.2359 1-4 EEL = 146302.8892 RESTRAINT = 0.0000 ESURF = 989.6961 minimization completed, ENE= -.56601620E+05 RMS= 0.173017E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2846.82 ( 4.95% of Gen B) | Calc gb diag 13792.96 (23.96% of Gen B) | Calc gb off-diag 40925.11 (71.09% of Gen B) | Gen Born time 57565.21 (100.0% of Nonbo) | Nonbond force 57565.21 (100.0% of Force) | Bond/Angle/Dihedral 17.19 ( 0.03% of Force) | Force time 57582.43 (100.0% of Runmd) | Runmd Time 57582.43 (99.85% of Total) | Other 87.60 ( 0.15% of Total) | Total time 57670.15 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:33:21.925 on 10/17/2010 | Setup done at 07:33:25.632 on 10/17/2010 | Run done at 23:34:32.074 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:33:15 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.21 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.21 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6718E+04 1.7330E+01 1.3001E+02 CD 2268 BOND = 8345.2124 ANGLE = 22239.5626 DIHED = 32276.7104 VDWAALS = -24065.6609 EEL = -190895.3188 EGB = -62513.7258 1-4 VDW = 10694.4896 1-4 EEL = 146214.4670 RESTRAINT = 0.0000 ESURF = 986.4452 minimization completed, ENE= -.56717819E+05 RMS= 0.173303E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6709E+04 1.7357E+01 1.3006E+02 N 4036 BOND = 8287.2669 ANGLE = 22080.6151 DIHED = 32456.7987 VDWAALS = -24131.3555 EEL = -190839.9769 EGB = -62594.7587 1-4 VDW = 10731.8414 1-4 EEL = 146312.3533 RESTRAINT = 0.0000 ESURF = 988.2083 minimization completed, ENE= -.56709007E+05 RMS= 0.173573E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6716E+04 1.7350E+01 1.2586E+02 CG 4706 BOND = 8398.1508 ANGLE = 22243.6634 DIHED = 32375.3452 VDWAALS = -24200.8080 EEL = -190824.3551 EGB = -62492.5361 1-4 VDW = 10678.4767 1-4 EEL = 146118.7596 RESTRAINT = 0.0000 ESURF = 987.3135 minimization completed, ENE= -.56715990E+05 RMS= 0.173505E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6425E+04 1.7338E+01 1.3192E+02 N 30463 BOND = 8474.5851 ANGLE = 22266.5672 DIHED = 32378.3800 VDWAALS = -23957.5392 EEL = -190533.3097 EGB = -62784.8855 1-4 VDW = 10691.8496 1-4 EEL = 146045.2004 RESTRAINT = 0.0000 ESURF = 994.5295 minimization completed, ENE= -.56424623E+05 RMS= 0.173384E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6544E+04 1.7286E+01 1.1986E+02 C 43777 BOND = 8375.1267 ANGLE = 22277.4906 DIHED = 32400.5338 VDWAALS = -24142.2983 EEL = -190839.0649 EGB = -62523.1202 1-4 VDW = 10769.8668 1-4 EEL = 146144.9908 RESTRAINT = 0.0000 ESURF = 992.1153 minimization completed, ENE= -.56544359E+05 RMS= 0.172859E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6940E+04 1.7288E+01 1.3019E+02 C 20729 BOND = 8369.3050 ANGLE = 22024.6423 DIHED = 32317.0376 VDWAALS = -24250.1753 EEL = -191162.9201 EGB = -62315.8483 1-4 VDW = 10733.3909 1-4 EEL = 146356.0572 RESTRAINT = 0.0000 ESURF = 988.4480 minimization completed, ENE= -.56940063E+05 RMS= 0.172877E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6878E+04 1.7264E+01 1.5218E+02 CG 9122 BOND = 8235.3688 ANGLE = 22144.7718 DIHED = 32381.9307 VDWAALS = -24332.5681 EEL = -190593.8001 EGB = -62561.9730 1-4 VDW = 10815.1397 1-4 EEL = 146046.8222 RESTRAINT = 0.0000 ESURF = 986.1249 minimization completed, ENE= -.56878183E+05 RMS= 0.172638E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6846E+04 1.7274E+01 1.2809E+02 C 16001 BOND = 8311.4202 ANGLE = 22138.9684 DIHED = 32348.9881 VDWAALS = -24210.6796 EEL = -191216.4713 EGB = -62185.4453 1-4 VDW = 10782.7670 1-4 EEL = 146203.7243 RESTRAINT = 0.0000 ESURF = 980.9539 minimization completed, ENE= -.56845774E+05 RMS= 0.172737E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6605E+04 1.7359E+01 1.2789E+02 C 13540 BOND = 8492.8127 ANGLE = 22083.7081 DIHED = 32378.9114 VDWAALS = -24233.4878 EEL = -190652.6367 EGB = -62657.6672 1-4 VDW = 10760.0669 1-4 EEL = 146242.3849 RESTRAINT = 0.0000 ESURF = 981.1996 minimization completed, ENE= -.56604708E+05 RMS= 0.173592E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6472E+04 1.7368E+01 1.3435E+02 C 8620 BOND = 8452.2830 ANGLE = 22211.5170 DIHED = 32485.8388 VDWAALS = -24214.0996 EEL = -190735.4035 EGB = -62624.3488 1-4 VDW = 10668.1713 1-4 EEL = 146299.0124 RESTRAINT = 0.0000 ESURF = 984.8189 minimization completed, ENE= -.56472211E+05 RMS= 0.173682E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6430E+04 1.7283E+01 1.1841E+02 C 17033 BOND = 8392.9383 ANGLE = 22381.7248 DIHED = 32424.4542 VDWAALS = -24274.6735 EEL = -190450.9146 EGB = -62731.2903 1-4 VDW = 10714.4260 1-4 EEL = 146126.7195 RESTRAINT = 0.0000 ESURF = 986.9068 minimization completed, ENE= -.56429709E+05 RMS= 0.172834E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6562E+04 1.7332E+01 1.2764E+02 C 8887 BOND = 8405.4760 ANGLE = 22154.1042 DIHED = 32491.6508 VDWAALS = -24111.4569 EEL = -190565.3423 EGB = -62922.5541 1-4 VDW = 10716.7990 1-4 EEL = 146282.4651 RESTRAINT = 0.0000 ESURF = 987.1648 minimization completed, ENE= -.56561694E+05 RMS= 0.173319E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6587E+04 1.7241E+01 1.2760E+02 N 11836 BOND = 8381.6324 ANGLE = 22225.2865 DIHED = 32395.9696 VDWAALS = -24027.5931 EEL = -190561.2379 EGB = -62807.4977 1-4 VDW = 10751.9774 1-4 EEL = 146068.1859 RESTRAINT = 0.0000 ESURF = 986.2975 minimization completed, ENE= -.56586979E+05 RMS= 0.172412E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6439E+04 1.7258E+01 1.3989E+02 CD 5312 BOND = 8344.1189 ANGLE = 22383.7558 DIHED = 32549.0939 VDWAALS = -24202.3863 EEL = -190345.2033 EGB = -62898.8509 1-4 VDW = 10667.0491 1-4 EEL = 146072.1970 RESTRAINT = 0.0000 ESURF = 990.7290 minimization completed, ENE= -.56439497E+05 RMS= 0.172580E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6561E+04 1.7420E+01 1.4297E+02 C 26004 BOND = 8449.7658 ANGLE = 22326.0521 DIHED = 32490.8008 VDWAALS = -24300.3409 EEL = -190208.5238 EGB = -62850.3047 1-4 VDW = 10706.2824 1-4 EEL = 145840.4883 RESTRAINT = 0.0000 ESURF = 984.2888 minimization completed, ENE= -.56561491E+05 RMS= 0.174204E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6655E+04 1.7248E+01 1.3947E+02 C 5029 BOND = 8350.2656 ANGLE = 22168.7103 DIHED = 32549.4845 VDWAALS = -24179.3241 EEL = -190446.8228 EGB = -62794.7790 1-4 VDW = 10709.0860 1-4 EEL = 146000.0558 RESTRAINT = 0.0000 ESURF = 988.2233 minimization completed, ENE= -.56655100E+05 RMS= 0.172478E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6330E+04 1.7329E+01 1.2953E+02 CD 13132 BOND = 8362.2411 ANGLE = 22358.0193 DIHED = 32354.4668 VDWAALS = -23993.9628 EEL = -190024.8259 EGB = -63229.2949 1-4 VDW = 10802.9152 1-4 EEL = 146052.5818 RESTRAINT = 0.0000 ESURF = 987.9284 minimization completed, ENE= -.56329931E+05 RMS= 0.173291E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6351E+04 1.7351E+01 1.3516E+02 C 1103 BOND = 8485.1180 ANGLE = 22271.1312 DIHED = 32431.3689 VDWAALS = -24178.1919 EEL = -190378.5732 EGB = -62984.4950 1-4 VDW = 10738.6665 1-4 EEL = 146272.5163 RESTRAINT = 0.0000 ESURF = 991.3909 minimization completed, ENE= -.56351068E+05 RMS= 0.173515E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6360E+04 1.7321E+01 1.3234E+02 N 36237 BOND = 8310.1981 ANGLE = 22351.7482 DIHED = 32371.3618 VDWAALS = -24190.1904 EEL = -190124.4863 EGB = -62959.6953 1-4 VDW = 10753.2433 1-4 EEL = 146136.1132 RESTRAINT = 0.0000 ESURF = 992.0772 minimization completed, ENE= -.56359630E+05 RMS= 0.173214E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6560E+04 1.7293E+01 1.3935E+02 C 10992 BOND = 8470.9268 ANGLE = 22117.9425 DIHED = 32460.9032 VDWAALS = -24103.2173 EEL = -190041.3722 EGB = -63168.2467 1-4 VDW = 10689.2088 1-4 EEL = 146018.8342 RESTRAINT = 0.0000 ESURF = 995.0053 minimization completed, ENE= -.56560015E+05 RMS= 0.172931E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6511E+04 1.7378E+01 1.3139E+02 CD 28936 BOND = 8460.4628 ANGLE = 22055.9293 DIHED = 32511.2184 VDWAALS = -24155.4568 EEL = -190741.1525 EGB = -62671.9443 1-4 VDW = 10745.0295 1-4 EEL = 146298.2934 RESTRAINT = 0.0000 ESURF = 987.0199 minimization completed, ENE= -.56510600E+05 RMS= 0.173781E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6316E+04 1.7408E+01 1.2106E+02 C 13556 BOND = 8412.6263 ANGLE = 22303.9245 DIHED = 32461.7126 VDWAALS = -24021.9641 EEL = -190501.3604 EGB = -62914.9430 1-4 VDW = 10812.9270 1-4 EEL = 146136.0399 RESTRAINT = 0.0000 ESURF = 995.3440 minimization completed, ENE= -.56315693E+05 RMS= 0.174075E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6810E+04 1.7211E+01 1.2416E+02 C 3999 BOND = 8251.9324 ANGLE = 22145.5712 DIHED = 32406.9293 VDWAALS = -24102.9947 EEL = -190387.9984 EGB = -62843.3945 1-4 VDW = 10743.5812 1-4 EEL = 145985.1601 RESTRAINT = 0.0000 ESURF = 991.4082 minimization completed, ENE= -.56809805E+05 RMS= 0.172112E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6482E+04 1.7262E+01 1.2117E+02 CG 8617 BOND = 8373.3393 ANGLE = 22194.9771 DIHED = 32487.1928 VDWAALS = -24139.1790 EEL = -190625.7954 EGB = -62831.2287 1-4 VDW = 10751.7738 1-4 EEL = 146315.3033 RESTRAINT = 0.0000 ESURF = 991.8218 minimization completed, ENE= -.56481795E+05 RMS= 0.172625E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6278E+04 1.7425E+01 1.5229E+02 C 30461 BOND = 8511.4814 ANGLE = 22364.4939 DIHED = 32392.1331 VDWAALS = -24009.6674 EEL = -190394.7749 EGB = -63083.9838 1-4 VDW = 10724.6045 1-4 EEL = 146226.9094 RESTRAINT = 0.0000 ESURF = 990.6598 minimization completed, ENE= -.56278144E+05 RMS= 0.174248E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2853.32 ( 4.95% of Gen B) | Calc gb diag 13763.79 (23.90% of Gen B) | Calc gb off-diag 40971.15 (71.14% of Gen B) | Gen Born time 57588.27 (100.0% of Nonbo) | Nonbond force 57588.27 (100.0% of Force) | Bond/Angle/Dihedral 16.80 ( 0.03% of Force) | Force time 57605.10 (100.0% of Runmd) | Runmd Time 57605.10 (99.84% of Total) | Other 90.37 ( 0.16% of Total) | Total time 57695.61 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:33:15.707 on 10/17/2010 | Setup done at 07:33:18.762 on 10/17/2010 | Run done at 23:34:51.314 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:33:08 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.20 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.20 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6541E+04 1.7366E+01 1.3842E+02 CD 32289 BOND = 8448.5608 ANGLE = 22393.8985 DIHED = 32447.8674 VDWAALS = -24169.2283 EEL = -190942.0173 EGB = -62402.1913 1-4 VDW = 10643.7009 1-4 EEL = 146050.9763 RESTRAINT = 0.0000 ESURF = 987.6717 minimization completed, ENE= -.56540761E+05 RMS= 0.173661E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6668E+04 1.7319E+01 1.2542E+02 C 1742 BOND = 8467.1981 ANGLE = 22201.8804 DIHED = 32397.1968 VDWAALS = -24039.1050 EEL = -190883.2727 EGB = -62611.3730 1-4 VDW = 10678.9300 1-4 EEL = 146128.5047 RESTRAINT = 0.0000 ESURF = 991.8576 minimization completed, ENE= -.56668183E+05 RMS= 0.173188E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6546E+04 1.7328E+01 1.3562E+02 CG 37846 BOND = 8365.7890 ANGLE = 22264.7311 DIHED = 32411.4953 VDWAALS = -24203.7513 EEL = -191007.4181 EGB = -62272.4783 1-4 VDW = 10777.9472 1-4 EEL = 146128.6217 RESTRAINT = 0.0000 ESURF = 988.9196 minimization completed, ENE= -.56546144E+05 RMS= 0.173283E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6395E+04 1.7370E+01 1.2295E+02 C 3552 BOND = 8514.1465 ANGLE = 22255.0904 DIHED = 32389.8958 VDWAALS = -24058.8030 EEL = -191132.8723 EGB = -62291.5805 1-4 VDW = 10784.4364 1-4 EEL = 146154.6842 RESTRAINT = 0.0000 ESURF = 990.2165 minimization completed, ENE= -.56394786E+05 RMS= 0.173701E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6559E+04 1.7281E+01 1.4682E+02 CG 13815 BOND = 8426.5196 ANGLE = 22409.3745 DIHED = 32409.8282 VDWAALS = -24103.2756 EEL = -190887.6888 EGB = -62621.4462 1-4 VDW = 10652.5049 1-4 EEL = 146167.4427 RESTRAINT = 0.0000 ESURF = 987.4032 minimization completed, ENE= -.56559337E+05 RMS= 0.172807E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6569E+04 1.7360E+01 1.3562E+02 C 34332 BOND = 8419.1600 ANGLE = 22364.6386 DIHED = 32490.6277 VDWAALS = -24167.6068 EEL = -190792.3696 EGB = -62606.1067 1-4 VDW = 10682.6683 1-4 EEL = 146054.3530 RESTRAINT = 0.0000 ESURF = 985.6577 minimization completed, ENE= -.56568978E+05 RMS= 0.173604E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6687E+04 1.7325E+01 1.2517E+02 C 4602 BOND = 8396.9184 ANGLE = 22012.6419 DIHED = 32452.4007 VDWAALS = -24051.2869 EEL = -190471.0781 EGB = -62850.9329 1-4 VDW = 10681.5112 1-4 EEL = 146152.4543 RESTRAINT = 0.0000 ESURF = 990.8549 minimization completed, ENE= -.56686517E+05 RMS= 0.173254E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6650E+04 1.7221E+01 1.3534E+02 C 23444 BOND = 8456.4956 ANGLE = 22260.0816 DIHED = 32366.1584 VDWAALS = -24092.9956 EEL = -190597.6992 EGB = -62873.5667 1-4 VDW = 10689.8203 1-4 EEL = 146149.4875 RESTRAINT = 0.0000 ESURF = 992.3028 minimization completed, ENE= -.56649915E+05 RMS= 0.172207E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6589E+04 1.7200E+01 1.5435E+02 CD 5041 BOND = 8205.1182 ANGLE = 22196.3346 DIHED = 32399.4779 VDWAALS = -24109.2548 EEL = -189961.0223 EGB = -63189.8673 1-4 VDW = 10802.1811 1-4 EEL = 146078.1205 RESTRAINT = 0.0000 ESURF = 989.6771 minimization completed, ENE= -.56589235E+05 RMS= 0.172000E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6451E+04 1.7323E+01 1.2490E+02 C 31982 BOND = 8376.0255 ANGLE = 22169.1572 DIHED = 32483.0602 VDWAALS = -23940.6676 EEL = -190403.0876 EGB = -63164.5746 1-4 VDW = 10700.8307 1-4 EEL = 146337.6536 RESTRAINT = 0.0000 ESURF = 990.4102 minimization completed, ENE= -.56451192E+05 RMS= 0.173229E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6416E+04 1.7341E+01 1.4967E+02 C 35339 BOND = 8491.9879 ANGLE = 22412.5919 DIHED = 32354.9147 VDWAALS = -24134.3050 EEL = -189904.9023 EGB = -63194.5476 1-4 VDW = 10588.6739 1-4 EEL = 145981.7544 RESTRAINT = 0.0000 ESURF = 987.4538 minimization completed, ENE= -.56416378E+05 RMS= 0.173414E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6511E+04 1.7378E+01 1.4186E+02 C 30560 BOND = 8571.7840 ANGLE = 22285.0790 DIHED = 32456.5894 VDWAALS = -24223.0524 EEL = -190285.1407 EGB = -62947.1652 1-4 VDW = 10587.7299 1-4 EEL = 146056.7397 RESTRAINT = 0.0000 ESURF = 985.9960 minimization completed, ENE= -.56511440E+05 RMS= 0.173779E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6505E+04 1.7396E+01 1.2403E+02 C 673 BOND = 8418.5059 ANGLE = 22262.8585 DIHED = 32405.1135 VDWAALS = -24227.5654 EEL = -190349.1843 EGB = -62943.0108 1-4 VDW = 10688.8799 1-4 EEL = 146252.5895 RESTRAINT = 0.0000 ESURF = 986.4383 minimization completed, ENE= -.56505375E+05 RMS= 0.173958E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6281E+04 1.7434E+01 1.3426E+02 CG 7309 BOND = 8454.8064 ANGLE = 22222.2582 DIHED = 32450.5931 VDWAALS = -24114.0824 EEL = -190452.2797 EGB = -63032.2841 1-4 VDW = 10763.7747 1-4 EEL = 146439.7047 RESTRAINT = 0.0000 ESURF = 986.8947 minimization completed, ENE= -.56280614E+05 RMS= 0.174338E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6468E+04 1.7321E+01 1.4142E+02 C 8954 BOND = 8411.4190 ANGLE = 22325.1884 DIHED = 32324.1126 VDWAALS = -24053.2442 EEL = -190141.7884 EGB = -63093.1837 1-4 VDW = 10686.6802 1-4 EEL = 146082.1861 RESTRAINT = 0.0000 ESURF = 990.6795 minimization completed, ENE= -.56467950E+05 RMS= 0.173215E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6675E+04 1.7296E+01 1.2752E+02 C 34226 BOND = 8301.6422 ANGLE = 22411.1320 DIHED = 32342.1924 VDWAALS = -24134.4196 EEL = -190525.7935 EGB = -62922.3296 1-4 VDW = 10707.8744 1-4 EEL = 146158.2535 RESTRAINT = 0.0000 ESURF = 986.0332 minimization completed, ENE= -.56675415E+05 RMS= 0.172957E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6690E+04 1.7273E+01 1.2601E+02 CG 30496 BOND = 8307.1984 ANGLE = 22196.8514 DIHED = 32461.6215 VDWAALS = -24128.7594 EEL = -190740.4756 EGB = -62830.3230 1-4 VDW = 10738.6756 1-4 EEL = 146320.8264 RESTRAINT = 0.0000 ESURF = 984.4661 minimization completed, ENE= -.56689919E+05 RMS= 0.172730E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6555E+04 1.7276E+01 1.2726E+02 C 17049 BOND = 8410.4986 ANGLE = 22177.3490 DIHED = 32580.6416 VDWAALS = -24255.3057 EEL = -190459.5390 EGB = -62986.6067 1-4 VDW = 10733.2667 1-4 EEL = 146259.3414 RESTRAINT = 0.0000 ESURF = 985.0259 minimization completed, ENE= -.56555328E+05 RMS= 0.172757E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6727E+04 1.7257E+01 1.2154E+02 C 34767 BOND = 8460.0729 ANGLE = 22078.6582 DIHED = 32440.3224 VDWAALS = -24156.1801 EEL = -190550.1268 EGB = -62942.0897 1-4 VDW = 10687.9153 1-4 EEL = 146264.4715 RESTRAINT = 0.0000 ESURF = 989.9338 minimization completed, ENE= -.56727023E+05 RMS= 0.172570E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6366E+04 1.7357E+01 1.2223E+02 CA 40116 BOND = 8503.3602 ANGLE = 22099.7806 DIHED = 32650.8129 VDWAALS = -24095.4416 EEL = -190380.5756 EGB = -62920.2059 1-4 VDW = 10679.2613 1-4 EEL = 146108.1203 RESTRAINT = 0.0000 ESURF = 988.9074 minimization completed, ENE= -.56365980E+05 RMS= 0.173565E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6315E+04 1.7412E+01 1.2787E+02 CZ 33075 BOND = 8430.7217 ANGLE = 22240.1867 DIHED = 32517.1182 VDWAALS = -24062.8752 EEL = -190621.4072 EGB = -62781.8475 1-4 VDW = 10707.5136 1-4 EEL = 146265.6620 RESTRAINT = 0.0000 ESURF = 990.1712 minimization completed, ENE= -.56314756E+05 RMS= 0.174116E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6656E+04 1.7370E+01 1.4490E+02 CZ 39446 BOND = 8360.9990 ANGLE = 22162.7939 DIHED = 32419.5503 VDWAALS = -24274.5526 EEL = -190686.2167 EGB = -62651.6015 1-4 VDW = 10808.1364 1-4 EEL = 146216.8429 RESTRAINT = 0.0000 ESURF = 987.9230 minimization completed, ENE= -.56656126E+05 RMS= 0.173702E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6751E+04 1.7335E+01 1.2864E+02 C 9865 BOND = 8429.1161 ANGLE = 22128.8855 DIHED = 32509.5988 VDWAALS = -24223.6543 EEL = -190588.5216 EGB = -62951.7394 1-4 VDW = 10682.0212 1-4 EEL = 146271.5038 RESTRAINT = 0.0000 ESURF = 991.6403 minimization completed, ENE= -.56751150E+05 RMS= 0.173354E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6884E+04 1.7224E+01 1.3828E+02 C 11564 BOND = 8364.1520 ANGLE = 22145.8511 DIHED = 32396.2529 VDWAALS = -24076.8399 EEL = -191045.1740 EGB = -62588.6433 1-4 VDW = 10670.2856 1-4 EEL = 146260.4538 RESTRAINT = 0.0000 ESURF = 989.2597 minimization completed, ENE= -.56884402E+05 RMS= 0.172238E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6423E+04 1.7375E+01 1.3379E+02 C 30697 BOND = 8440.5990 ANGLE = 22261.1591 DIHED = 32369.8740 VDWAALS = -24187.9937 EEL = -190759.8916 EGB = -62794.9281 1-4 VDW = 10838.5289 1-4 EEL = 146422.1640 RESTRAINT = 0.0000 ESURF = 987.5727 minimization completed, ENE= -.56422916E+05 RMS= 0.173748E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2854.28 ( 4.95% of Gen B) | Calc gb diag 13756.35 (23.86% of Gen B) | Calc gb off-diag 41041.81 (71.19% of Gen B) | Gen Born time 57652.75 (100.0% of Nonbo) | Nonbond force 57652.75 (100.0% of Force) | Bond/Angle/Dihedral 17.40 ( 0.03% of Force) | Force time 57670.18 (100.0% of Runmd) | Runmd Time 57670.18 (99.85% of Total) | Other 85.13 ( 0.15% of Total) | Total time 57755.43 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:33:08.541 on 10/17/2010 | Setup done at 07:33:12.272 on 10/17/2010 | Run done at 23:35:43.973 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:33:02 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.19 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.19 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6520E+04 1.7316E+01 1.2918E+02 C 21292 BOND = 8351.8182 ANGLE = 22392.8275 DIHED = 32420.6861 VDWAALS = -24050.5103 EEL = -190508.9862 EGB = -63021.1889 1-4 VDW = 10698.2641 1-4 EEL = 146203.3712 RESTRAINT = 0.0000 ESURF = 994.0140 minimization completed, ENE= -.56519704E+05 RMS= 0.173156E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6222E+04 1.7281E+01 1.3386E+02 C 4484 BOND = 8424.8839 ANGLE = 22423.8410 DIHED = 32454.0888 VDWAALS = -24185.7877 EEL = -190527.5180 EGB = -62855.0982 1-4 VDW = 10770.2477 1-4 EEL = 146287.8351 RESTRAINT = 0.0000 ESURF = 985.9568 minimization completed, ENE= -.56221551E+05 RMS= 0.172808E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6575E+04 1.7251E+01 1.3835E+02 CD 4614 BOND = 8347.5195 ANGLE = 22309.0292 DIHED = 32365.5700 VDWAALS = -24213.2109 EEL = -190633.4653 EGB = -62652.8336 1-4 VDW = 10720.5114 1-4 EEL = 146199.5878 RESTRAINT = 0.0000 ESURF = 982.4465 minimization completed, ENE= -.56574845E+05 RMS= 0.172511E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6528E+04 1.7249E+01 1.2684E+02 CD 41993 BOND = 8374.4030 ANGLE = 22152.3392 DIHED = 32369.0526 VDWAALS = -24041.1854 EEL = -190947.3642 EGB = -62429.2449 1-4 VDW = 10757.0619 1-4 EEL = 146255.8251 RESTRAINT = 0.0000 ESURF = 980.8837 minimization completed, ENE= -.56528229E+05 RMS= 0.172490E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6653E+04 1.7314E+01 1.2077E+02 C 9260 BOND = 8286.8172 ANGLE = 22421.0731 DIHED = 32305.9475 VDWAALS = -24138.8710 EEL = -190723.5488 EGB = -62549.0881 1-4 VDW = 10684.8796 1-4 EEL = 146080.4520 RESTRAINT = 0.0000 ESURF = 979.3329 minimization completed, ENE= -.56653006E+05 RMS= 0.173139E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6531E+04 1.7387E+01 1.3058E+02 C 40426 BOND = 8466.6613 ANGLE = 22194.3018 DIHED = 32405.7871 VDWAALS = -24032.6539 EEL = -190578.3364 EGB = -62804.7077 1-4 VDW = 10711.6693 1-4 EEL = 146116.2375 RESTRAINT = 0.0000 ESURF = 990.0429 minimization completed, ENE= -.56530998E+05 RMS= 0.173872E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6555E+04 1.7396E+01 1.1761E+02 C 13643 BOND = 8376.4104 ANGLE = 22272.4677 DIHED = 32343.1295 VDWAALS = -24159.9918 EEL = -190859.4846 EGB = -62622.4114 1-4 VDW = 10765.0643 1-4 EEL = 146348.8514 RESTRAINT = 0.0000 ESURF = 981.2798 minimization completed, ENE= -.56554685E+05 RMS= 0.173965E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6479E+04 1.7375E+01 1.4317E+02 C 17903 BOND = 8523.3869 ANGLE = 22208.9402 DIHED = 32387.5496 VDWAALS = -24176.3345 EEL = -190810.0381 EGB = -62659.6329 1-4 VDW = 10749.4728 1-4 EEL = 146309.0089 RESTRAINT = 0.0000 ESURF = 988.8409 minimization completed, ENE= -.56478806E+05 RMS= 0.173753E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6589E+04 1.7403E+01 1.2563E+02 C 19238 BOND = 8380.3744 ANGLE = 22285.3837 DIHED = 32374.2846 VDWAALS = -24067.0944 EEL = -191075.8344 EGB = -62668.2152 1-4 VDW = 10746.8956 1-4 EEL = 146451.8373 RESTRAINT = 0.0000 ESURF = 983.2753 minimization completed, ENE= -.56589093E+05 RMS= 0.174026E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6658E+04 1.7357E+01 1.2598E+02 C 8553 BOND = 8332.7137 ANGLE = 22289.5325 DIHED = 32386.9636 VDWAALS = -24214.2709 EEL = -190907.1078 EGB = -62631.9236 1-4 VDW = 10769.8751 1-4 EEL = 146335.6263 RESTRAINT = 0.0000 ESURF = 980.4739 minimization completed, ENE= -.56658117E+05 RMS= 0.173566E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6712E+04 1.7347E+01 1.3183E+02 C 33953 BOND = 8286.9512 ANGLE = 22297.8096 DIHED = 32263.3152 VDWAALS = -24103.0073 EEL = -190964.0533 EGB = -62580.5458 1-4 VDW = 10764.8378 1-4 EEL = 146336.5297 RESTRAINT = 0.0000 ESURF = 985.8492 minimization completed, ENE= -.56712314E+05 RMS= 0.173469E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6821E+04 1.7349E+01 1.2823E+02 C 6526 BOND = 8426.4775 ANGLE = 22070.1492 DIHED = 32440.5057 VDWAALS = -24102.0131 EEL = -190948.6317 EGB = -62591.4418 1-4 VDW = 10691.3946 1-4 EEL = 146211.5077 RESTRAINT = 0.0000 ESURF = 981.3009 minimization completed, ENE= -.56820751E+05 RMS= 0.173489E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6265E+04 1.7372E+01 1.3043E+02 C 45357 BOND = 8461.4369 ANGLE = 22370.4668 DIHED = 32454.1076 VDWAALS = -24102.5191 EEL = -190910.3535 EGB = -62427.6475 1-4 VDW = 10720.9702 1-4 EEL = 146183.8212 RESTRAINT = 0.0000 ESURF = 984.9419 minimization completed, ENE= -.56264775E+05 RMS= 0.173717E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6491E+04 1.7349E+01 1.1851E+02 CD 2672 BOND = 8336.9009 ANGLE = 22330.6769 DIHED = 32322.3657 VDWAALS = -24141.4721 EEL = -190834.3825 EGB = -62509.0958 1-4 VDW = 10734.4821 1-4 EEL = 146286.3018 RESTRAINT = 0.0000 ESURF = 983.5473 minimization completed, ENE= -.56490676E+05 RMS= 0.173493E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6529E+04 1.7280E+01 1.4262E+02 CD 29999 BOND = 8368.5460 ANGLE = 22363.9806 DIHED = 32347.3867 VDWAALS = -24056.2887 EEL = -190741.7344 EGB = -62777.2894 1-4 VDW = 10720.0633 1-4 EEL = 146259.7976 RESTRAINT = 0.0000 ESURF = 986.5756 minimization completed, ENE= -.56528963E+05 RMS= 0.172802E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6547E+04 1.7409E+01 1.2792E+02 CG 30367 BOND = 8464.7759 ANGLE = 22196.4753 DIHED = 32254.3864 VDWAALS = -24174.8255 EEL = -190941.1524 EGB = -62302.3277 1-4 VDW = 10784.3343 1-4 EEL = 146189.0701 RESTRAINT = 0.0000 ESURF = 982.3305 minimization completed, ENE= -.56546933E+05 RMS= 0.174086E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6636E+04 1.7286E+01 1.1567E+02 C 32703 BOND = 8282.3452 ANGLE = 22263.8808 DIHED = 32453.4810 VDWAALS = -24054.6736 EEL = -191045.6883 EGB = -62426.5680 1-4 VDW = 10754.2642 1-4 EEL = 146151.9903 RESTRAINT = 0.0000 ESURF = 985.3615 minimization completed, ENE= -.56635607E+05 RMS= 0.172859E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6478E+04 1.7374E+01 1.3942E+02 N 25984 BOND = 8381.2618 ANGLE = 22374.8874 DIHED = 32422.2278 VDWAALS = -24056.0343 EEL = -191291.6407 EGB = -62124.4515 1-4 VDW = 10686.4588 1-4 EEL = 146146.7905 RESTRAINT = 0.0000 ESURF = 982.3925 minimization completed, ENE= -.56478108E+05 RMS= 0.173735E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6587E+04 1.7405E+01 1.2789E+02 C 7452 BOND = 8357.8421 ANGLE = 22332.8347 DIHED = 32331.9827 VDWAALS = -24238.5451 EEL = -190967.6516 EGB = -62457.0312 1-4 VDW = 10811.9105 1-4 EEL = 146257.6986 RESTRAINT = 0.0000 ESURF = 983.5083 minimization completed, ENE= -.56587451E+05 RMS= 0.174048E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6642E+04 1.7287E+01 1.3591E+02 C 22343 BOND = 8285.8702 ANGLE = 22255.4304 DIHED = 32358.0361 VDWAALS = -24147.8293 EEL = -190838.5179 EGB = -62527.3459 1-4 VDW = 10743.1635 1-4 EEL = 146250.4417 RESTRAINT = 0.0000 ESURF = 978.9269 minimization completed, ENE= -.56641824E+05 RMS= 0.172872E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6730E+04 1.7240E+01 1.2742E+02 CA 4301 BOND = 8350.5874 ANGLE = 22213.8949 DIHED = 32448.5084 VDWAALS = -24239.0458 EEL = -191379.5910 EGB = -62306.1504 1-4 VDW = 10783.5167 1-4 EEL = 146414.9950 RESTRAINT = 0.0000 ESURF = 983.1896 minimization completed, ENE= -.56730095E+05 RMS= 0.172400E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6607E+04 1.7179E+01 1.2336E+02 C 29153 BOND = 8347.3082 ANGLE = 22309.7328 DIHED = 32401.7208 VDWAALS = -24127.8412 EEL = -191116.9399 EGB = -62501.8903 1-4 VDW = 10779.9967 1-4 EEL = 146314.1780 RESTRAINT = 0.0000 ESURF = 986.9773 minimization completed, ENE= -.56606757E+05 RMS= 0.171786E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6658E+04 1.7357E+01 1.3100E+02 C 4949 BOND = 8414.5295 ANGLE = 22336.9844 DIHED = 32343.8329 VDWAALS = -24120.7925 EEL = -191364.8932 EGB = -62249.8665 1-4 VDW = 10705.6066 1-4 EEL = 146287.5094 RESTRAINT = 0.0000 ESURF = 989.2961 minimization completed, ENE= -.56657793E+05 RMS= 0.173570E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6542E+04 1.7309E+01 1.2553E+02 N 6208 BOND = 8392.7605 ANGLE = 22210.5581 DIHED = 32316.0552 VDWAALS = -24045.0813 EEL = -191148.7568 EGB = -62316.3772 1-4 VDW = 10755.6340 1-4 EEL = 146308.9058 RESTRAINT = 0.0000 ESURF = 984.5936 minimization completed, ENE= -.56541708E+05 RMS= 0.173092E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6698E+04 1.7304E+01 1.2410E+02 C 21747 BOND = 8411.6749 ANGLE = 22161.7086 DIHED = 32407.3526 VDWAALS = -24118.0684 EEL = -190534.5963 EGB = -62901.3944 1-4 VDW = 10711.1241 1-4 EEL = 146173.8953 RESTRAINT = 0.0000 ESURF = 989.8434 minimization completed, ENE= -.56698460E+05 RMS= 0.173040E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2861.52 ( 4.97% of Gen B) | Calc gb diag 13845.82 (24.04% of Gen B) | Calc gb off-diag 40899.11 (71.00% of Gen B) | Gen Born time 57606.46 (100.0% of Nonbo) | Nonbond force 57606.46 (100.0% of Force) | Bond/Angle/Dihedral 16.30 ( 0.03% of Force) | Force time 57623.09 (100.0% of Runmd) | Runmd Time 57623.09 (99.86% of Total) | Other 82.16 ( 0.14% of Total) | Total time 57705.38 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:33:02.201 on 10/17/2010 | Setup done at 07:33:04.503 on 10/17/2010 | Run done at 23:34:47.585 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:32:55 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.18 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.18 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6589E+04 1.7346E+01 1.4080E+02 C 17795 BOND = 8463.3692 ANGLE = 22254.2035 DIHED = 32223.8068 VDWAALS = -24154.3281 EEL = -190462.0235 EGB = -63098.3929 1-4 VDW = 10725.9577 1-4 EEL = 146478.2319 RESTRAINT = 0.0000 ESURF = 979.7629 minimization completed, ENE= -.56589412E+05 RMS= 0.173457E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6393E+04 1.7405E+01 1.2970E+02 C 41629 BOND = 8358.6823 ANGLE = 22382.5028 DIHED = 32321.5868 VDWAALS = -24034.9574 EEL = -191009.7170 EGB = -62457.1200 1-4 VDW = 10809.0510 1-4 EEL = 146251.7747 RESTRAINT = 0.0000 ESURF = 985.2569 minimization completed, ENE= -.56392940E+05 RMS= 0.174052E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6331E+04 1.7396E+01 1.2697E+02 C 29127 BOND = 8527.8609 ANGLE = 22251.1440 DIHED = 32339.3604 VDWAALS = -24149.1619 EEL = -190649.9959 EGB = -62748.3253 1-4 VDW = 10712.2289 1-4 EEL = 146402.4314 RESTRAINT = 0.0000 ESURF = 983.4373 minimization completed, ENE= -.56331020E+05 RMS= 0.173961E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6595E+04 1.7276E+01 1.1709E+02 CG 3293 BOND = 8278.2101 ANGLE = 22240.5782 DIHED = 32397.9441 VDWAALS = -24118.9614 EEL = -190675.3230 EGB = -62929.3563 1-4 VDW = 10779.2701 1-4 EEL = 146442.5745 RESTRAINT = 0.0000 ESURF = 990.3249 minimization completed, ENE= -.56594739E+05 RMS= 0.172756E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.7051E+04 1.7231E+01 1.3163E+02 C 33436 BOND = 8345.3286 ANGLE = 22033.5828 DIHED = 32350.9756 VDWAALS = -24168.5818 EEL = -190845.6097 EGB = -62836.6516 1-4 VDW = 10699.7250 1-4 EEL = 146386.0115 RESTRAINT = 0.0000 ESURF = 984.3193 minimization completed, ENE= -.57050900E+05 RMS= 0.172305E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6446E+04 1.7266E+01 1.2230E+02 C 3710 BOND = 8368.0019 ANGLE = 22136.2669 DIHED = 32249.8094 VDWAALS = -24144.7577 EEL = -190213.7241 EGB = -63071.4778 1-4 VDW = 10804.8495 1-4 EEL = 146440.8708 RESTRAINT = 0.0000 ESURF = 984.5951 minimization completed, ENE= -.56445566E+05 RMS= 0.172658E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6354E+04 1.7289E+01 1.2511E+02 C 45805 BOND = 8251.2606 ANGLE = 22423.1279 DIHED = 32418.8464 VDWAALS = -24152.1649 EEL = -190476.6528 EGB = -62764.0353 1-4 VDW = 10751.1731 1-4 EEL = 146219.3840 RESTRAINT = 0.0000 ESURF = 975.5540 minimization completed, ENE= -.56353507E+05 RMS= 0.172890E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6656E+04 1.7352E+01 1.3785E+02 C 23855 BOND = 8315.6512 ANGLE = 22224.9240 DIHED = 32375.7588 VDWAALS = -24108.2196 EEL = -190547.2430 EGB = -63011.5743 1-4 VDW = 10743.0546 1-4 EEL = 146369.2733 RESTRAINT = 0.0000 ESURF = 982.2771 minimization completed, ENE= -.56656098E+05 RMS= 0.173516E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6503E+04 1.7341E+01 1.1846E+02 CG 2429 BOND = 8395.8105 ANGLE = 22351.9530 DIHED = 32312.9965 VDWAALS = -24159.5323 EEL = -190524.4700 EGB = -62752.1711 1-4 VDW = 10745.4861 1-4 EEL = 146146.6959 RESTRAINT = 0.0000 ESURF = 979.9986 minimization completed, ENE= -.56503233E+05 RMS= 0.173411E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6390E+04 1.7371E+01 1.4302E+02 N 8789 BOND = 8425.2772 ANGLE = 22317.4840 DIHED = 32572.9627 VDWAALS = -24074.7083 EEL = -190535.0283 EGB = -62992.7715 1-4 VDW = 10684.4062 1-4 EEL = 146228.3549 RESTRAINT = 0.0000 ESURF = 984.4634 minimization completed, ENE= -.56389560E+05 RMS= 0.173706E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6551E+04 1.7358E+01 1.1967E+02 CG 11598 BOND = 8369.9805 ANGLE = 22322.0938 DIHED = 32388.7477 VDWAALS = -24214.9631 EEL = -190318.2212 EGB = -63089.6960 1-4 VDW = 10749.7024 1-4 EEL = 146262.0595 RESTRAINT = 0.0000 ESURF = 979.7516 minimization completed, ENE= -.56550545E+05 RMS= 0.173582E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6614E+04 1.7291E+01 1.2106E+02 C 3729 BOND = 8383.7951 ANGLE = 22316.0289 DIHED = 32313.5049 VDWAALS = -24227.9876 EEL = -190361.2601 EGB = -62946.3209 1-4 VDW = 10700.3164 1-4 EEL = 146226.2658 RESTRAINT = 0.0000 ESURF = 981.5039 minimization completed, ENE= -.56614153E+05 RMS= 0.172907E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6683E+04 1.7255E+01 1.2894E+02 CD 38882 BOND = 8299.3958 ANGLE = 22313.4481 DIHED = 32252.6389 VDWAALS = -24168.7145 EEL = -190854.4826 EGB = -62638.0189 1-4 VDW = 10769.0094 1-4 EEL = 146362.4953 RESTRAINT = 0.0000 ESURF = 981.0659 minimization completed, ENE= -.56683163E+05 RMS= 0.172553E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6782E+04 1.7248E+01 1.2849E+02 CZ 45841 BOND = 8360.6792 ANGLE = 22207.7035 DIHED = 32294.1693 VDWAALS = -24179.4046 EEL = -190249.7686 EGB = -63118.9929 1-4 VDW = 10752.2045 1-4 EEL = 146168.3678 RESTRAINT = 0.0000 ESURF = 983.2650 minimization completed, ENE= -.56781777E+05 RMS= 0.172479E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6784E+04 1.7251E+01 1.2815E+02 CZ 14129 BOND = 8390.5018 ANGLE = 21978.2001 DIHED = 32460.1561 VDWAALS = -24117.3555 EEL = -190897.3750 EGB = -62578.3067 1-4 VDW = 10690.1867 1-4 EEL = 146309.8448 RESTRAINT = 0.0000 ESURF = 980.3030 minimization completed, ENE= -.56783845E+05 RMS= 0.172509E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6362E+04 1.7380E+01 1.2915E+02 C 19800 BOND = 8426.9536 ANGLE = 22379.5499 DIHED = 32367.5870 VDWAALS = -24171.3630 EEL = -190078.8999 EGB = -63287.5836 1-4 VDW = 10745.9433 1-4 EEL = 146276.0193 RESTRAINT = 0.0000 ESURF = 979.3783 minimization completed, ENE= -.56362415E+05 RMS= 0.173796E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6824E+04 1.7268E+01 1.2180E+02 C 4808 BOND = 8376.5848 ANGLE = 22194.9671 DIHED = 32450.2812 VDWAALS = -24206.5148 EEL = -190611.2929 EGB = -62760.7941 1-4 VDW = 10661.2353 1-4 EEL = 146090.9764 RESTRAINT = 0.0000 ESURF = 980.5147 minimization completed, ENE= -.56824042E+05 RMS= 0.172677E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6506E+04 1.7365E+01 1.4157E+02 CD 8988 BOND = 8499.1268 ANGLE = 22369.5759 DIHED = 32320.9383 VDWAALS = -24211.0364 EEL = -189670.5364 EGB = -63700.1900 1-4 VDW = 10705.6480 1-4 EEL = 146201.1733 RESTRAINT = 0.0000 ESURF = 978.8558 minimization completed, ENE= -.56506445E+05 RMS= 0.173650E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6747E+04 1.7413E+01 1.3245E+02 C 4345 BOND = 8516.0175 ANGLE = 22083.4959 DIHED = 32205.9365 VDWAALS = -24177.1955 EEL = -190184.6832 EGB = -63144.5644 1-4 VDW = 10744.2977 1-4 EEL = 146230.4992 RESTRAINT = 0.0000 ESURF = 979.6176 minimization completed, ENE= -.56746579E+05 RMS= 0.174134E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6395E+04 1.7317E+01 1.3238E+02 CD 40193 BOND = 8357.6947 ANGLE = 22315.7325 DIHED = 32409.1175 VDWAALS = -24170.4176 EEL = -190285.8072 EGB = -63114.9663 1-4 VDW = 10689.8949 1-4 EEL = 146419.0108 RESTRAINT = 0.0000 ESURF = 985.1404 minimization completed, ENE= -.56394600E+05 RMS= 0.173169E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6430E+04 1.7350E+01 1.2833E+02 CE1 32005 BOND = 8360.0752 ANGLE = 22297.3163 DIHED = 32450.8326 VDWAALS = -24108.4094 EEL = -190322.4107 EGB = -63037.1744 1-4 VDW = 10787.7523 1-4 EEL = 146164.4280 RESTRAINT = 0.0000 ESURF = 977.4403 minimization completed, ENE= -.56430150E+05 RMS= 0.173497E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6524E+04 1.7253E+01 1.1685E+02 CD 28992 BOND = 8479.0473 ANGLE = 22132.3104 DIHED = 32456.0910 VDWAALS = -24213.8325 EEL = -190254.8846 EGB = -62947.0693 1-4 VDW = 10663.9109 1-4 EEL = 146180.8140 RESTRAINT = 0.0000 ESURF = 980.1081 minimization completed, ENE= -.56523505E+05 RMS= 0.172531E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6450E+04 1.7304E+01 1.2353E+02 CD 14356 BOND = 8354.8709 ANGLE = 22289.4187 DIHED = 32396.3780 VDWAALS = -24038.5026 EEL = -190510.9059 EGB = -62949.2896 1-4 VDW = 10820.8371 1-4 EEL = 146203.1253 RESTRAINT = 0.0000 ESURF = 984.2329 minimization completed, ENE= -.56449835E+05 RMS= 0.173038E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6524E+04 1.7289E+01 1.2796E+02 C 2096 BOND = 8387.1948 ANGLE = 22099.9310 DIHED = 32458.9057 VDWAALS = -24180.1057 EEL = -190375.5866 EGB = -62789.7133 1-4 VDW = 10739.7280 1-4 EEL = 146149.2492 RESTRAINT = 0.0000 ESURF = 986.3154 minimization completed, ENE= -.56524082E+05 RMS= 0.172890E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6352E+04 1.7295E+01 1.2271E+02 C 2499 BOND = 8265.6963 ANGLE = 22392.1319 DIHED = 32403.2197 VDWAALS = -24174.3565 EEL = -190528.7888 EGB = -62820.2412 1-4 VDW = 10727.5855 1-4 EEL = 146393.1289 RESTRAINT = 0.0000 ESURF = 990.0376 minimization completed, ENE= -.56351587E+05 RMS= 0.172953E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2993.52 ( 5.20% of Gen B) | Calc gb diag 13874.68 (24.11% of Gen B) | Calc gb off-diag 40688.53 (70.69% of Gen B) | Gen Born time 57556.74 (100.0% of Nonbo) | Nonbond force 57556.74 (100.0% of Force) | Bond/Angle/Dihedral 17.34 ( 0.03% of Force) | Force time 57574.11 (100.0% of Runmd) | Runmd Time 57574.11 (99.85% of Total) | Other 88.65 ( 0.15% of Total) | Total time 57662.98 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:32:55.453 on 10/17/2010 | Setup done at 07:32:59.010 on 10/17/2010 | Run done at 23:33:58.431 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:32:48 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.17 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.17 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6374E+04 1.7390E+01 1.2633E+02 CD 2818 BOND = 8460.4125 ANGLE = 22304.8547 DIHED = 32414.0864 VDWAALS = -24168.8708 EEL = -190012.5082 EGB = -63342.5788 1-4 VDW = 10666.4452 1-4 EEL = 146318.5270 RESTRAINT = 0.0000 ESURF = 985.4129 minimization completed, ENE= -.56374219E+05 RMS= 0.173902E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6593E+04 1.7278E+01 1.2908E+02 C 20859 BOND = 8421.4251 ANGLE = 22357.5061 DIHED = 32419.2048 VDWAALS = -24175.9383 EEL = -190517.4066 EGB = -62898.5701 1-4 VDW = 10650.0300 1-4 EEL = 146169.1204 RESTRAINT = 0.0000 ESURF = 982.1230 minimization completed, ENE= -.56592506E+05 RMS= 0.172780E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6462E+04 1.7336E+01 1.3293E+02 C 2514 BOND = 8334.8829 ANGLE = 22261.9633 DIHED = 32357.1608 VDWAALS = -24234.8050 EEL = -190385.3144 EGB = -62997.3737 1-4 VDW = 10799.8093 1-4 EEL = 146422.4753 RESTRAINT = 0.0000 ESURF = 979.3078 minimization completed, ENE= -.56461894E+05 RMS= 0.173364E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6573E+04 1.7254E+01 1.1719E+02 C 44682 BOND = 8300.2156 ANGLE = 22170.0296 DIHED = 32377.8160 VDWAALS = -24129.0434 EEL = -190589.9213 EGB = -62953.7764 1-4 VDW = 10718.6487 1-4 EEL = 146553.5289 RESTRAINT = 0.0000 ESURF = 979.2678 minimization completed, ENE= -.56573235E+05 RMS= 0.172539E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6497E+04 1.7350E+01 1.4386E+02 CG 2610 BOND = 8463.7696 ANGLE = 22333.1186 DIHED = 32402.8379 VDWAALS = -24123.5007 EEL = -190484.2614 EGB = -63031.5615 1-4 VDW = 10752.6962 1-4 EEL = 146209.5374 RESTRAINT = 0.0000 ESURF = 980.5655 minimization completed, ENE= -.56496798E+05 RMS= 0.173498E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6539E+04 1.7369E+01 1.2637E+02 C 18493 BOND = 8536.1246 ANGLE = 22091.0853 DIHED = 32393.4613 VDWAALS = -23999.6410 EEL = -190701.3366 EGB = -62907.8105 1-4 VDW = 10765.4113 1-4 EEL = 146293.7813 RESTRAINT = 0.0000 ESURF = 989.6323 minimization completed, ENE= -.56539292E+05 RMS= 0.173690E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6423E+04 1.7326E+01 1.3727E+02 CD 10103 BOND = 8384.8994 ANGLE = 22275.7561 DIHED = 32421.5815 VDWAALS = -24156.7985 EEL = -190072.3873 EGB = -63193.5674 1-4 VDW = 10759.1077 1-4 EEL = 146169.6002 RESTRAINT = 0.0000 ESURF = 988.5957 minimization completed, ENE= -.56423213E+05 RMS= 0.173264E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6544E+04 1.7374E+01 1.2183E+02 CG 27675 BOND = 8375.8525 ANGLE = 22302.2220 DIHED = 32476.5322 VDWAALS = -24184.3540 EEL = -190462.7483 EGB = -63137.8648 1-4 VDW = 10733.8895 1-4 EEL = 146366.8205 RESTRAINT = 0.0000 ESURF = 986.0240 minimization completed, ENE= -.56543626E+05 RMS= 0.173739E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6468E+04 1.7317E+01 1.0964E+02 C 24113 BOND = 8338.9833 ANGLE = 22365.6571 DIHED = 32446.9209 VDWAALS = -24147.4493 EEL = -190511.3249 EGB = -62926.0067 1-4 VDW = 10713.9795 1-4 EEL = 146271.7223 RESTRAINT = 0.0000 ESURF = 979.3193 minimization completed, ENE= -.56468199E+05 RMS= 0.173168E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6475E+04 1.7460E+01 1.3566E+02 CG 22741 BOND = 8512.9167 ANGLE = 22294.9523 DIHED = 32394.8800 VDWAALS = -24241.4642 EEL = -190265.1231 EGB = -63108.4114 1-4 VDW = 10711.9343 1-4 EEL = 146243.1444 RESTRAINT = 0.0000 ESURF = 982.1951 minimization completed, ENE= -.56474976E+05 RMS= 0.174599E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6497E+04 1.7323E+01 1.3196E+02 C 2256 BOND = 8428.5260 ANGLE = 22243.8177 DIHED = 32375.8524 VDWAALS = -24182.0057 EEL = -190396.8454 EGB = -62908.5087 1-4 VDW = 10679.8829 1-4 EEL = 146283.1396 RESTRAINT = 0.0000 ESURF = 979.4862 minimization completed, ENE= -.56496655E+05 RMS= 0.173228E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6433E+04 1.7429E+01 1.3529E+02 CG 25282 BOND = 8453.8897 ANGLE = 22280.8716 DIHED = 32416.2105 VDWAALS = -24200.5098 EEL = -190580.0293 EGB = -62916.4454 1-4 VDW = 10759.5538 1-4 EEL = 146369.6268 RESTRAINT = 0.0000 ESURF = 983.5066 minimization completed, ENE= -.56433326E+05 RMS= 0.174295E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6654E+04 1.7296E+01 1.2660E+02 C 41271 BOND = 8355.1733 ANGLE = 22248.3201 DIHED = 32389.6037 VDWAALS = -24126.3344 EEL = -190700.7157 EGB = -62751.9254 1-4 VDW = 10719.9616 1-4 EEL = 146228.4332 RESTRAINT = 0.0000 ESURF = 983.8731 minimization completed, ENE= -.56653610E+05 RMS= 0.172960E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6670E+04 1.7367E+01 1.1938E+02 CZ 36565 BOND = 8458.6607 ANGLE = 22252.6954 DIHED = 32378.4437 VDWAALS = -24217.4079 EEL = -190757.6391 EGB = -62848.4654 1-4 VDW = 10701.6210 1-4 EEL = 146379.5754 RESTRAINT = 0.0000 ESURF = 982.3926 minimization completed, ENE= -.56670124E+05 RMS= 0.173670E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6603E+04 1.7341E+01 1.3951E+02 CG 1248 BOND = 8360.1066 ANGLE = 22295.6056 DIHED = 32362.9317 VDWAALS = -24272.9315 EEL = -190449.3039 EGB = -62858.1102 1-4 VDW = 10683.2133 1-4 EEL = 146299.5996 RESTRAINT = 0.0000 ESURF = 975.5487 minimization completed, ENE= -.56603340E+05 RMS= 0.173412E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6638E+04 1.7347E+01 1.3027E+02 CD 7727 BOND = 8364.8258 ANGLE = 22108.5473 DIHED = 32457.3737 VDWAALS = -24143.1570 EEL = -190294.7814 EGB = -63187.9950 1-4 VDW = 10722.2532 1-4 EEL = 146355.1994 RESTRAINT = 0.0000 ESURF = 979.4096 minimization completed, ENE= -.56638324E+05 RMS= 0.173471E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6406E+04 1.7223E+01 1.2963E+02 N 3693 BOND = 8275.3042 ANGLE = 22417.6842 DIHED = 32419.3825 VDWAALS = -24144.8458 EEL = -190275.1803 EGB = -63210.5346 1-4 VDW = 10774.4478 1-4 EEL = 146354.4302 RESTRAINT = 0.0000 ESURF = 983.6922 minimization completed, ENE= -.56405620E+05 RMS= 0.172232E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6507E+04 1.7349E+01 1.3955E+02 C 16323 BOND = 8360.6181 ANGLE = 22418.4551 DIHED = 32389.1373 VDWAALS = -24167.1364 EEL = -190476.8092 EGB = -63159.9348 1-4 VDW = 10743.4906 1-4 EEL = 146395.2827 RESTRAINT = 0.0000 ESURF = 990.1047 minimization completed, ENE= -.56506792E+05 RMS= 0.173494E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6608E+04 1.7361E+01 1.2722E+02 C 11362 BOND = 8278.0226 ANGLE = 22207.7672 DIHED = 32435.8894 VDWAALS = -24245.2805 EEL = -190292.2732 EGB = -63167.2539 1-4 VDW = 10799.5684 1-4 EEL = 146391.1418 RESTRAINT = 0.0000 ESURF = 984.1491 minimization completed, ENE= -.56608269E+05 RMS= 0.173611E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6483E+04 1.7310E+01 1.2881E+02 C 46115 BOND = 8352.8844 ANGLE = 22494.2686 DIHED = 32387.2102 VDWAALS = -24219.0452 EEL = -190424.1891 EGB = -63048.3613 1-4 VDW = 10681.0740 1-4 EEL = 146311.2322 RESTRAINT = 0.0000 ESURF = 981.4740 minimization completed, ENE= -.56483452E+05 RMS= 0.173105E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6573E+04 1.7451E+01 1.3977E+02 C 2301 BOND = 8549.2669 ANGLE = 22294.5699 DIHED = 32364.9574 VDWAALS = -24244.8852 EEL = -190209.8840 EGB = -63108.5086 1-4 VDW = 10623.7143 1-4 EEL = 146177.2416 RESTRAINT = 0.0000 ESURF = 980.3773 minimization completed, ENE= -.56573151E+05 RMS= 0.174510E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6412E+04 1.7390E+01 1.2823E+02 C 40955 BOND = 8320.9942 ANGLE = 22344.9239 DIHED = 32406.4241 VDWAALS = -24217.1598 EEL = -190758.0994 EGB = -62611.1566 1-4 VDW = 10809.2598 1-4 EEL = 146316.6384 RESTRAINT = 0.0000 ESURF = 976.0812 minimization completed, ENE= -.56412094E+05 RMS= 0.173899E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6631E+04 1.7342E+01 1.3124E+02 CD 30724 BOND = 8369.5818 ANGLE = 22159.8807 DIHED = 32421.2117 VDWAALS = -24176.0919 EEL = -191006.4789 EGB = -62375.4768 1-4 VDW = 10699.4498 1-4 EEL = 146298.2513 RESTRAINT = 0.0000 ESURF = 978.4005 minimization completed, ENE= -.56631272E+05 RMS= 0.173423E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6616E+04 1.7248E+01 1.2400E+02 C 45091 BOND = 8366.6254 ANGLE = 22091.9292 DIHED = 32411.5158 VDWAALS = -24233.9599 EEL = -190579.2628 EGB = -62807.7610 1-4 VDW = 10765.0456 1-4 EEL = 146389.3075 RESTRAINT = 0.0000 ESURF = 980.2933 minimization completed, ENE= -.56616267E+05 RMS= 0.172484E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6479E+04 1.7426E+01 1.3235E+02 C 5232 BOND = 8452.3998 ANGLE = 22310.4546 DIHED = 32237.0270 VDWAALS = -24130.4708 EEL = -190261.8319 EGB = -63098.1384 1-4 VDW = 10736.0609 1-4 EEL = 146292.9067 RESTRAINT = 0.0000 ESURF = 982.7231 minimization completed, ENE= -.56478869E+05 RMS= 0.174259E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2871.63 ( 5.00% of Gen B) | Calc gb diag 13974.48 (24.33% of Gen B) | Calc gb off-diag 40602.07 (70.68% of Gen B) | Gen Born time 57448.19 (100.0% of Nonbo) | Nonbond force 57448.19 (100.0% of Force) | Bond/Angle/Dihedral 17.38 ( 0.03% of Force) | Force time 57465.60 (100.0% of Runmd) | Runmd Time 57465.60 (99.84% of Total) | Other 90.93 ( 0.16% of Total) | Total time 57556.65 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:32:48.553 on 10/17/2010 | Setup done at 07:32:51.974 on 10/17/2010 | Run done at 23:32:05.203 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:32:42 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.16 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.16 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6439E+04 1.7421E+01 1.3453E+02 C 20379 BOND = 8512.1308 ANGLE = 22323.2434 DIHED = 32484.0190 VDWAALS = -24151.8125 EEL = -190794.9538 EGB = -62704.1106 1-4 VDW = 10698.4088 1-4 EEL = 146215.3488 RESTRAINT = 0.0000 ESURF = 978.3731 minimization completed, ENE= -.56439353E+05 RMS= 0.174207E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6432E+04 1.7349E+01 1.3482E+02 C 43082 BOND = 8458.8088 ANGLE = 22340.5585 DIHED = 32375.9698 VDWAALS = -24300.6592 EEL = -190498.3169 EGB = -62849.0139 1-4 VDW = 10749.9931 1-4 EEL = 146313.6698 RESTRAINT = 0.0000 ESURF = 976.6621 minimization completed, ENE= -.56432328E+05 RMS= 0.173488E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6737E+04 1.7330E+01 1.3611E+02 C 2378 BOND = 8413.0076 ANGLE = 21962.6857 DIHED = 32372.9049 VDWAALS = -24188.1147 EEL = -190365.5758 EGB = -62995.5807 1-4 VDW = 10774.6175 1-4 EEL = 146309.3054 RESTRAINT = 0.0000 ESURF = 980.2049 minimization completed, ENE= -.56736545E+05 RMS= 0.173304E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6651E+04 1.7209E+01 1.2202E+02 C 9728 BOND = 8302.1827 ANGLE = 22234.1058 DIHED = 32483.8871 VDWAALS = -24235.0648 EEL = -190598.3346 EGB = -62766.1246 1-4 VDW = 10732.1782 1-4 EEL = 146211.5251 RESTRAINT = 0.0000 ESURF = 984.3432 minimization completed, ENE= -.56651302E+05 RMS= 0.172093E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6694E+04 1.7289E+01 1.2011E+02 CD 30724 BOND = 8365.1612 ANGLE = 22383.7690 DIHED = 32336.0817 VDWAALS = -24181.0716 EEL = -190275.0467 EGB = -63021.3070 1-4 VDW = 10660.3329 1-4 EEL = 146055.6941 RESTRAINT = 0.0000 ESURF = 982.1076 minimization completed, ENE= -.56694279E+05 RMS= 0.172890E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6741E+04 1.7286E+01 1.2283E+02 C 27215 BOND = 8347.4244 ANGLE = 22221.3434 DIHED = 32366.9775 VDWAALS = -24275.5290 EEL = -189990.2240 EGB = -63109.2259 1-4 VDW = 10641.3188 1-4 EEL = 146073.1647 RESTRAINT = 0.0000 ESURF = 983.2930 minimization completed, ENE= -.56741457E+05 RMS= 0.172857E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6187E+04 1.7346E+01 1.3389E+02 C 1069 BOND = 8466.9131 ANGLE = 22340.3825 DIHED = 32454.1587 VDWAALS = -24194.9050 EEL = -190280.5197 EGB = -62826.9180 1-4 VDW = 10788.9603 1-4 EEL = 146087.8625 RESTRAINT = 0.0000 ESURF = 976.8489 minimization completed, ENE= -.56187217E+05 RMS= 0.173463E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6753E+04 1.7282E+01 1.3614E+02 C 808 BOND = 8270.9705 ANGLE = 22032.6666 DIHED = 32361.2990 VDWAALS = -24212.2316 EEL = -190423.7698 EGB = -62902.8667 1-4 VDW = 10818.5193 1-4 EEL = 146328.1574 RESTRAINT = 0.0000 ESURF = 974.4878 minimization completed, ENE= -.56752767E+05 RMS= 0.172816E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6735E+04 1.7372E+01 1.3712E+02 C 19323 BOND = 8328.2982 ANGLE = 22159.8689 DIHED = 32278.2374 VDWAALS = -24213.8582 EEL = -190282.7580 EGB = -63255.5287 1-4 VDW = 10800.2458 1-4 EEL = 146476.7169 RESTRAINT = 0.0000 ESURF = 974.1037 minimization completed, ENE= -.56734674E+05 RMS= 0.173720E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6521E+04 1.7413E+01 1.4215E+02 N 20216 BOND = 8460.9226 ANGLE = 22197.5636 DIHED = 32432.5373 VDWAALS = -24212.6718 EEL = -190578.7365 EGB = -62896.3090 1-4 VDW = 10753.8580 1-4 EEL = 146349.8073 RESTRAINT = 0.0000 ESURF = 971.7117 minimization completed, ENE= -.56521317E+05 RMS= 0.174132E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6581E+04 1.7405E+01 1.3765E+02 CD 34475 BOND = 8460.7402 ANGLE = 22332.0285 DIHED = 32381.0671 VDWAALS = -24244.4884 EEL = -190708.1473 EGB = -62619.8159 1-4 VDW = 10706.1376 1-4 EEL = 146133.0448 RESTRAINT = 0.0000 ESURF = 978.3443 minimization completed, ENE= -.56581089E+05 RMS= 0.174047E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6421E+04 1.7295E+01 1.2467E+02 C 26932 BOND = 8357.4025 ANGLE = 22454.5018 DIHED = 32347.8605 VDWAALS = -24243.2577 EEL = -190720.2374 EGB = -62622.7278 1-4 VDW = 10791.2589 1-4 EEL = 146237.5605 RESTRAINT = 0.0000 ESURF = 976.3538 minimization completed, ENE= -.56421285E+05 RMS= 0.172955E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6618E+04 1.7333E+01 1.2561E+02 C 45168 BOND = 8381.8450 ANGLE = 22365.3074 DIHED = 32377.6774 VDWAALS = -24312.5720 EEL = -190698.3858 EGB = -62628.4239 1-4 VDW = 10780.2873 1-4 EEL = 146138.5425 RESTRAINT = 0.0000 ESURF = 977.2471 minimization completed, ENE= -.56618475E+05 RMS= 0.173334E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6667E+04 1.7280E+01 1.2509E+02 C 22059 BOND = 8296.3724 ANGLE = 22301.7209 DIHED = 32446.7518 VDWAALS = -24321.0505 EEL = -190610.5218 EGB = -62572.0482 1-4 VDW = 10729.8928 1-4 EEL = 146086.0982 RESTRAINT = 0.0000 ESURF = 975.6507 minimization completed, ENE= -.56667134E+05 RMS= 0.172804E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6807E+04 1.7360E+01 1.3315E+02 CD 22889 BOND = 8368.3290 ANGLE = 22280.1707 DIHED = 32345.7626 VDWAALS = -24309.6048 EEL = -190540.3636 EGB = -62774.0476 1-4 VDW = 10757.1554 1-4 EEL = 146088.9518 RESTRAINT = 0.0000 ESURF = 976.6577 minimization completed, ENE= -.56806989E+05 RMS= 0.173602E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6636E+04 1.7434E+01 1.2013E+02 C 35358 BOND = 8465.3707 ANGLE = 22286.9238 DIHED = 32362.4342 VDWAALS = -24306.4739 EEL = -190604.7551 EGB = -62660.8922 1-4 VDW = 10732.8919 1-4 EEL = 146107.0053 RESTRAINT = 0.0000 ESURF = 981.6776 minimization completed, ENE= -.56635818E+05 RMS= 0.174335E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6690E+04 1.7365E+01 1.3487E+02 C 44034 BOND = 8476.1271 ANGLE = 22142.9442 DIHED = 32254.8348 VDWAALS = -24179.9084 EEL = -190539.9711 EGB = -62875.8211 1-4 VDW = 10735.9561 1-4 EEL = 146313.9193 RESTRAINT = 0.0000 ESURF = 982.2970 minimization completed, ENE= -.56689622E+05 RMS= 0.173650E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6634E+04 1.7263E+01 1.1828E+02 C 5315 BOND = 8428.7863 ANGLE = 22123.8612 DIHED = 32437.9247 VDWAALS = -24172.8013 EEL = -190659.6712 EGB = -62664.6327 1-4 VDW = 10696.9589 1-4 EEL = 146193.5102 RESTRAINT = 0.0000 ESURF = 982.4964 minimization completed, ENE= -.56633567E+05 RMS= 0.172634E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6744E+04 1.7297E+01 1.2554E+02 C 28073 BOND = 8434.9039 ANGLE = 22235.7956 DIHED = 32360.9172 VDWAALS = -24180.9699 EEL = -190752.1075 EGB = -62692.7117 1-4 VDW = 10697.4064 1-4 EEL = 146170.4711 RESTRAINT = 0.0000 ESURF = 982.1711 minimization completed, ENE= -.56744124E+05 RMS= 0.172967E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6761E+04 1.7304E+01 1.2748E+02 C 31395 BOND = 8359.6470 ANGLE = 22228.4909 DIHED = 32324.7856 VDWAALS = -24144.1363 EEL = -191218.4853 EGB = -62347.6598 1-4 VDW = 10726.3527 1-4 EEL = 146327.6314 RESTRAINT = 0.0000 ESURF = 982.4678 minimization completed, ENE= -.56760906E+05 RMS= 0.173036E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6750E+04 1.7267E+01 1.3187E+02 C 41017 BOND = 8389.2942 ANGLE = 22287.4091 DIHED = 32358.4505 VDWAALS = -24239.2251 EEL = -190481.3776 EGB = -63025.0469 1-4 VDW = 10716.8729 1-4 EEL = 146259.3559 RESTRAINT = 0.0000 ESURF = 984.3411 minimization completed, ENE= -.56749926E+05 RMS= 0.172672E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6550E+04 1.7341E+01 1.4297E+02 N 46062 BOND = 8407.9889 ANGLE = 22314.0599 DIHED = 32443.4340 VDWAALS = -24151.2045 EEL = -190615.8834 EGB = -62992.9583 1-4 VDW = 10769.9652 1-4 EEL = 146290.0837 RESTRAINT = 0.0000 ESURF = 984.1480 minimization completed, ENE= -.56550367E+05 RMS= 0.173412E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6823E+04 1.7234E+01 1.3614E+02 C 29127 BOND = 8339.2581 ANGLE = 22182.9214 DIHED = 32342.1795 VDWAALS = -24075.8872 EEL = -190756.3609 EGB = -62935.8256 1-4 VDW = 10713.9037 1-4 EEL = 146385.1614 RESTRAINT = 0.0000 ESURF = 981.5038 minimization completed, ENE= -.56823146E+05 RMS= 0.172338E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6685E+04 1.7486E+01 1.3084E+02 C 34122 BOND = 8423.1760 ANGLE = 22173.2320 DIHED = 32373.9200 VDWAALS = -24031.8837 EEL = -190821.0253 EGB = -62926.4130 1-4 VDW = 10713.8549 1-4 EEL = 146426.7565 RESTRAINT = 0.0000 ESURF = 983.4083 minimization completed, ENE= -.56684974E+05 RMS= 0.174860E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6236E+04 1.7454E+01 1.3720E+02 C 19810 BOND = 8535.0907 ANGLE = 22426.8191 DIHED = 32373.2259 VDWAALS = -24118.4593 EEL = -190463.1738 EGB = -63058.7638 1-4 VDW = 10733.0935 1-4 EEL = 146351.6740 RESTRAINT = 0.0000 ESURF = 984.2327 minimization completed, ENE= -.56236261E+05 RMS= 0.174544E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2886.68 ( 5.01% of Gen B) | Calc gb diag 13821.24 (24.00% of Gen B) | Calc gb off-diag 40892.43 (70.99% of Gen B) | Gen Born time 57600.36 (100.0% of Nonbo) | Nonbond force 57600.36 (100.0% of Force) | Bond/Angle/Dihedral 15.73 ( 0.03% of Force) | Force time 57616.13 (100.0% of Runmd) | Runmd Time 57616.13 (99.84% of Total) | Other 89.91 ( 0.16% of Total) | Total time 57706.16 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:32:42.758 on 10/17/2010 | Setup done at 07:32:45.588 on 10/17/2010 | Run done at 23:34:28.919 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:32:35 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.15 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.15 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6647E+04 1.7345E+01 1.3464E+02 C 2432 BOND = 8443.5037 ANGLE = 22186.2268 DIHED = 32399.8486 VDWAALS = -24112.0535 EEL = -190347.4717 EGB = -63128.3512 1-4 VDW = 10722.5690 1-4 EEL = 146199.8748 RESTRAINT = 0.0000 ESURF = 988.6459 minimization completed, ENE= -.56647208E+05 RMS= 0.173455E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6638E+04 1.7209E+01 1.3348E+02 CD 13975 BOND = 8313.6153 ANGLE = 22197.2357 DIHED = 32400.5033 VDWAALS = -24163.1870 EEL = -190371.5806 EGB = -62925.2802 1-4 VDW = 10771.4784 1-4 EEL = 146153.1160 RESTRAINT = 0.0000 ESURF = 986.1926 minimization completed, ENE= -.56637907E+05 RMS= 0.172091E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6521E+04 1.7363E+01 1.2337E+02 N 21400 BOND = 8459.7645 ANGLE = 22189.1287 DIHED = 32412.0098 VDWAALS = -24167.9781 EEL = -190439.5177 EGB = -63048.8315 1-4 VDW = 10769.1264 1-4 EEL = 146318.7291 RESTRAINT = 0.0000 ESURF = 986.8168 minimization completed, ENE= -.56520752E+05 RMS= 0.173626E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6171E+04 1.7426E+01 1.4362E+02 C 8680 BOND = 8450.0413 ANGLE = 22483.0846 DIHED = 32492.1930 VDWAALS = -24174.0920 EEL = -190042.4284 EGB = -63033.2501 1-4 VDW = 10631.7297 1-4 EEL = 146036.3509 RESTRAINT = 0.0000 ESURF = 985.7886 minimization completed, ENE= -.56170582E+05 RMS= 0.174261E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6659E+04 1.7284E+01 1.2574E+02 N 11977 BOND = 8363.2606 ANGLE = 22299.4778 DIHED = 32467.8972 VDWAALS = -24190.2029 EEL = -189874.1784 EGB = -63293.0609 1-4 VDW = 10669.4287 1-4 EEL = 145913.1704 RESTRAINT = 0.0000 ESURF = 985.2950 minimization completed, ENE= -.56658913E+05 RMS= 0.172837E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6617E+04 1.7243E+01 1.2845E+02 C 17009 BOND = 8288.8453 ANGLE = 22132.5697 DIHED = 32552.1931 VDWAALS = -24117.5287 EEL = -190219.7637 EGB = -63143.6224 1-4 VDW = 10762.5047 1-4 EEL = 146145.5458 RESTRAINT = 0.0000 ESURF = 982.4628 minimization completed, ENE= -.56616793E+05 RMS= 0.172430E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6681E+04 1.7255E+01 1.2751E+02 C 12209 BOND = 8391.4559 ANGLE = 22295.2205 DIHED = 32326.8272 VDWAALS = -24231.5588 EEL = -190235.7682 EGB = -63119.3878 1-4 VDW = 10742.6525 1-4 EEL = 146163.3656 RESTRAINT = 0.0000 ESURF = 986.4833 minimization completed, ENE= -.56680710E+05 RMS= 0.172549E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6511E+04 1.7337E+01 1.1856E+02 CD 10908 BOND = 8405.1775 ANGLE = 22187.7526 DIHED = 32383.8572 VDWAALS = -24056.0217 EEL = -190347.8409 EGB = -63252.8507 1-4 VDW = 10786.6513 1-4 EEL = 146400.1975 RESTRAINT = 0.0000 ESURF = 982.0594 minimization completed, ENE= -.56511018E+05 RMS= 0.173365E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6356E+04 1.7466E+01 1.6263E+02 C 26702 BOND = 8560.5393 ANGLE = 22347.1267 DIHED = 32473.9841 VDWAALS = -24151.0701 EEL = -190055.7962 EGB = -63121.1503 1-4 VDW = 10635.6237 1-4 EEL = 145967.1158 RESTRAINT = 0.0000 ESURF = 987.5208 minimization completed, ENE= -.56356106E+05 RMS= 0.174659E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6690E+04 1.7285E+01 1.1640E+02 CD 44606 BOND = 8381.9697 ANGLE = 22283.3002 DIHED = 32305.3131 VDWAALS = -24247.1268 EEL = -190298.1963 EGB = -63095.5416 1-4 VDW = 10733.6008 1-4 EEL = 146262.9398 RESTRAINT = 0.0000 ESURF = 984.0273 minimization completed, ENE= -.56689714E+05 RMS= 0.172848E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6667E+04 1.7363E+01 1.4436E+02 CG 30814 BOND = 8455.0822 ANGLE = 22306.8293 DIHED = 32527.6518 VDWAALS = -24227.2391 EEL = -189958.7019 EGB = -63390.1838 1-4 VDW = 10650.6281 1-4 EEL = 145982.2925 RESTRAINT = 0.0000 ESURF = 986.4751 minimization completed, ENE= -.56667166E+05 RMS= 0.173626E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6664E+04 1.7301E+01 1.2078E+02 C 24491 BOND = 8457.4407 ANGLE = 22262.9612 DIHED = 32424.3041 VDWAALS = -24265.2867 EEL = -190103.6510 EGB = -63204.0184 1-4 VDW = 10672.5374 1-4 EEL = 146111.1629 RESTRAINT = 0.0000 ESURF = 980.6577 minimization completed, ENE= -.56663892E+05 RMS= 0.173006E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6348E+04 1.7284E+01 1.3122E+02 N 38390 BOND = 8343.0270 ANGLE = 22469.2445 DIHED = 32445.6091 VDWAALS = -24133.6448 EEL = -190569.8983 EGB = -62652.6357 1-4 VDW = 10736.2189 1-4 EEL = 146030.5935 RESTRAINT = 0.0000 ESURF = 983.5156 minimization completed, ENE= -.56347970E+05 RMS= 0.172845E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6659E+04 1.7222E+01 1.2059E+02 C 7207 BOND = 8296.7615 ANGLE = 22393.8103 DIHED = 32402.3909 VDWAALS = -24155.0813 EEL = -190455.3339 EGB = -62890.7276 1-4 VDW = 10686.1152 1-4 EEL = 146077.6549 RESTRAINT = 0.0000 ESURF = 985.1270 minimization completed, ENE= -.56659283E+05 RMS= 0.172219E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6208E+04 1.7401E+01 1.3983E+02 C 44790 BOND = 8548.9352 ANGLE = 22427.5131 DIHED = 32450.6725 VDWAALS = -24101.3328 EEL = -190182.7410 EGB = -63204.1621 1-4 VDW = 10700.6095 1-4 EEL = 146163.5456 RESTRAINT = 0.0000 ESURF = 988.5042 minimization completed, ENE= -.56208456E+05 RMS= 0.174005E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6375E+04 1.7380E+01 1.3054E+02 N 28773 BOND = 8432.6992 ANGLE = 22353.5206 DIHED = 32476.5994 VDWAALS = -24207.7231 EEL = -190246.8116 EGB = -62970.2662 1-4 VDW = 10690.5092 1-4 EEL = 146113.9307 RESTRAINT = 0.0000 ESURF = 982.6361 minimization completed, ENE= -.56374906E+05 RMS= 0.173799E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6307E+04 1.7349E+01 1.3759E+02 C 29602 BOND = 8423.6618 ANGLE = 22348.3990 DIHED = 32390.9677 VDWAALS = -24194.6104 EEL = -190049.1106 EGB = -63144.3141 1-4 VDW = 10779.8352 1-4 EEL = 146154.3242 RESTRAINT = 0.0000 ESURF = 984.2706 minimization completed, ENE= -.56306577E+05 RMS= 0.173493E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6597E+04 1.7231E+01 1.2690E+02 C 28257 BOND = 8377.8732 ANGLE = 22054.6173 DIHED = 32341.0629 VDWAALS = -24051.4279 EEL = -190018.6034 EGB = -63186.5602 1-4 VDW = 10742.2371 1-4 EEL = 146158.1155 RESTRAINT = 0.0000 ESURF = 985.5582 minimization completed, ENE= -.56597127E+05 RMS= 0.172313E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6768E+04 1.7241E+01 1.1832E+02 C 18596 BOND = 8296.9329 ANGLE = 22239.9925 DIHED = 32415.2436 VDWAALS = -24249.0228 EEL = -190219.3019 EGB = -63123.3104 1-4 VDW = 10753.1473 1-4 EEL = 146136.5297 RESTRAINT = 0.0000 ESURF = 982.2412 minimization completed, ENE= -.56767548E+05 RMS= 0.172413E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6613E+04 1.7368E+01 1.2970E+02 CD 5805 BOND = 8363.3652 ANGLE = 22178.3958 DIHED = 32458.9614 VDWAALS = -24263.8336 EEL = -190104.6034 EGB = -63108.6356 1-4 VDW = 10689.6454 1-4 EEL = 146190.1094 RESTRAINT = 0.0000 ESURF = 983.8560 minimization completed, ENE= -.56612739E+05 RMS= 0.173678E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6437E+04 1.7306E+01 1.2182E+02 N 12500 BOND = 8427.9549 ANGLE = 22182.2904 DIHED = 32558.6905 VDWAALS = -24252.4961 EEL = -189850.2703 EGB = -63385.3224 1-4 VDW = 10730.8181 1-4 EEL = 146160.2674 RESTRAINT = 0.0000 ESURF = 990.8121 minimization completed, ENE= -.56437255E+05 RMS= 0.173064E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6490E+04 1.7333E+01 1.2940E+02 CD 30217 BOND = 8415.1835 ANGLE = 22380.6809 DIHED = 32351.3421 VDWAALS = -24210.4337 EEL = -189885.7548 EGB = -63350.4227 1-4 VDW = 10685.4886 1-4 EEL = 146139.0402 RESTRAINT = 0.0000 ESURF = 984.5930 minimization completed, ENE= -.56490283E+05 RMS= 0.173331E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6619E+04 1.7172E+01 1.1317E+02 C 43539 BOND = 8340.2059 ANGLE = 21987.7130 DIHED = 32464.9538 VDWAALS = -24147.7536 EEL = -190180.1796 EGB = -63179.5059 1-4 VDW = 10769.2400 1-4 EEL = 146340.7962 RESTRAINT = 0.0000 ESURF = 985.8327 minimization completed, ENE= -.56618697E+05 RMS= 0.171723E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6739E+04 1.7259E+01 1.3098E+02 CG 9885 BOND = 8312.2225 ANGLE = 22179.8613 DIHED = 32437.5983 VDWAALS = -24186.7216 EEL = -190190.3382 EGB = -63117.7363 1-4 VDW = 10723.6861 1-4 EEL = 146118.4588 RESTRAINT = 0.0000 ESURF = 983.7987 minimization completed, ENE= -.56739170E+05 RMS= 0.172591E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6463E+04 1.7353E+01 1.2471E+02 C 35480 BOND = 8490.9580 ANGLE = 22122.1627 DIHED = 32408.1806 VDWAALS = -24108.8744 EEL = -189980.4695 EGB = -63197.8904 1-4 VDW = 10685.0519 1-4 EEL = 146126.6199 RESTRAINT = 0.0000 ESURF = 990.8655 minimization completed, ENE= -.56463396E+05 RMS= 0.173526E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2852.50 ( 4.97% of Gen B) | Calc gb diag 13959.10 (24.32% of Gen B) | Calc gb off-diag 40593.59 (70.71% of Gen B) | Gen Born time 57405.21 (100.0% of Nonbo) | Nonbond force 57405.21 (100.0% of Force) | Bond/Angle/Dihedral 18.07 ( 0.03% of Force) | Force time 57423.31 (100.0% of Runmd) | Runmd Time 57423.31 (99.84% of Total) | Other 93.95 ( 0.16% of Total) | Total time 57517.39 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:32:35.491 on 10/17/2010 | Setup done at 07:32:39.246 on 10/17/2010 | Run done at 23:31:12.877 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:32:29 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.14 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.14 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6538E+04 1.7333E+01 1.2419E+02 C 42743 BOND = 8269.2878 ANGLE = 22413.1458 DIHED = 32402.5718 VDWAALS = -24101.6668 EEL = -190320.2681 EGB = -63146.4313 1-4 VDW = 10731.3008 1-4 EEL = 146231.3242 RESTRAINT = 0.0000 ESURF = 982.5079 minimization completed, ENE= -.56538228E+05 RMS= 0.173327E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6411E+04 1.7303E+01 1.3830E+02 C 41384 BOND = 8307.5823 ANGLE = 22210.5764 DIHED = 32435.2570 VDWAALS = -24134.2575 EEL = -190497.5547 EGB = -62901.5031 1-4 VDW = 10840.5847 1-4 EEL = 146345.2933 RESTRAINT = 0.0000 ESURF = 982.6269 minimization completed, ENE= -.56411395E+05 RMS= 0.173031E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6693E+04 1.7237E+01 1.4355E+02 C 31351 BOND = 8349.5090 ANGLE = 22274.0637 DIHED = 32348.4267 VDWAALS = -24086.6109 EEL = -190397.1012 EGB = -63097.7229 1-4 VDW = 10699.8701 1-4 EEL = 146229.9052 RESTRAINT = 0.0000 ESURF = 986.7557 minimization completed, ENE= -.56692905E+05 RMS= 0.172370E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6381E+04 1.7299E+01 1.2899E+02 C 28844 BOND = 8457.6246 ANGLE = 22127.1675 DIHED = 32403.4384 VDWAALS = -24148.8620 EEL = -189857.4195 EGB = -63294.6819 1-4 VDW = 10715.1714 1-4 EEL = 146233.7302 RESTRAINT = 0.0000 ESURF = 983.3246 minimization completed, ENE= -.56380507E+05 RMS= 0.172993E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6502E+04 1.7324E+01 1.3009E+02 N 1400 BOND = 8478.2253 ANGLE = 22074.2214 DIHED = 32377.5458 VDWAALS = -24194.1352 EEL = -190102.5531 EGB = -63178.3533 1-4 VDW = 10752.2501 1-4 EEL = 146307.5579 RESTRAINT = 0.0000 ESURF = 983.2229 minimization completed, ENE= -.56502018E+05 RMS= 0.173239E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6384E+04 1.7302E+01 1.3468E+02 C 46949 BOND = 8380.6955 ANGLE = 22484.7928 DIHED = 32497.0385 VDWAALS = -24161.0038 EEL = -190224.3153 EGB = -63085.3009 1-4 VDW = 10661.3046 1-4 EEL = 146079.1796 RESTRAINT = 0.0000 ESURF = 983.2463 minimization completed, ENE= -.56384363E+05 RMS= 0.173022E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6497E+04 1.7357E+01 1.3033E+02 CD 34119 BOND = 8397.3816 ANGLE = 22353.1705 DIHED = 32387.5618 VDWAALS = -24059.0460 EEL = -190733.1250 EGB = -62580.5576 1-4 VDW = 10657.5276 1-4 EEL = 146096.4132 RESTRAINT = 0.0000 ESURF = 983.4545 minimization completed, ENE= -.56497219E+05 RMS= 0.173573E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6419E+04 1.7426E+01 1.2067E+02 N 40198 BOND = 8563.4137 ANGLE = 22322.9766 DIHED = 32316.5745 VDWAALS = -24107.3182 EEL = -190406.1370 EGB = -62915.2226 1-4 VDW = 10679.7497 1-4 EEL = 146140.5857 RESTRAINT = 0.0000 ESURF = 986.8558 minimization completed, ENE= -.56418522E+05 RMS= 0.174263E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6422E+04 1.7295E+01 1.1774E+02 CD 22874 BOND = 8322.9850 ANGLE = 22195.9427 DIHED = 32427.6129 VDWAALS = -23982.5127 EEL = -190551.6899 EGB = -63189.0150 1-4 VDW = 10834.3946 1-4 EEL = 146524.0606 RESTRAINT = 0.0000 ESURF = 996.4714 minimization completed, ENE= -.56421750E+05 RMS= 0.172947E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6613E+04 1.7279E+01 1.2198E+02 C 15467 BOND = 8399.6889 ANGLE = 22324.6011 DIHED = 32335.1472 VDWAALS = -24030.6211 EEL = -190856.5354 EGB = -62780.6609 1-4 VDW = 10681.8649 1-4 EEL = 146321.8469 RESTRAINT = 0.0000 ESURF = 991.5613 minimization completed, ENE= -.56613107E+05 RMS= 0.172791E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6415E+04 1.7366E+01 1.3442E+02 C 33896 BOND = 8478.4825 ANGLE = 22329.6120 DIHED = 32462.7257 VDWAALS = -24219.9753 EEL = -190727.7407 EGB = -62712.9015 1-4 VDW = 10692.6067 1-4 EEL = 146296.6519 RESTRAINT = 0.0000 ESURF = 985.0848 minimization completed, ENE= -.56415454E+05 RMS= 0.173658E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6459E+04 1.7406E+01 1.4176E+02 NE 6664 BOND = 8433.9661 ANGLE = 22175.7781 DIHED = 32414.1368 VDWAALS = -24174.3471 EEL = -190463.7784 EGB = -62933.0961 1-4 VDW = 10762.4785 1-4 EEL = 146338.8772 RESTRAINT = 0.0000 ESURF = 987.1368 minimization completed, ENE= -.56458848E+05 RMS= 0.174059E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6329E+04 1.7376E+01 1.1533E+02 C 23217 BOND = 8440.8018 ANGLE = 22216.3967 DIHED = 32504.1898 VDWAALS = -24131.8499 EEL = -190476.1907 EGB = -62987.6252 1-4 VDW = 10705.9758 1-4 EEL = 146413.4495 RESTRAINT = 0.0000 ESURF = 985.8089 minimization completed, ENE= -.56329043E+05 RMS= 0.173755E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6368E+04 1.7458E+01 1.3677E+02 C 45626 BOND = 8579.0587 ANGLE = 22192.2750 DIHED = 32361.8916 VDWAALS = -24075.2428 EEL = -191054.3948 EGB = -62660.3367 1-4 VDW = 10740.6569 1-4 EEL = 146559.7090 RESTRAINT = 0.0000 ESURF = 988.4668 minimization completed, ENE= -.56367916E+05 RMS= 0.174585E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6413E+04 1.7408E+01 1.4446E+02 CA 8459 BOND = 8444.3657 ANGLE = 22194.6063 DIHED = 32369.7276 VDWAALS = -24043.1659 EEL = -190645.4924 EGB = -62766.8421 1-4 VDW = 10729.0164 1-4 EEL = 146320.8545 RESTRAINT = 0.0000 ESURF = 984.4153 minimization completed, ENE= -.56412515E+05 RMS= 0.174080E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6428E+04 1.7320E+01 1.2920E+02 C 3672 BOND = 8337.3000 ANGLE = 22402.4425 DIHED = 32430.6601 VDWAALS = -24129.3203 EEL = -190199.9333 EGB = -63203.4627 1-4 VDW = 10734.1572 1-4 EEL = 146212.0572 RESTRAINT = 0.0000 ESURF = 988.1948 minimization completed, ENE= -.56427904E+05 RMS= 0.173197E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6692E+04 1.7364E+01 1.3404E+02 CD 18060 BOND = 8390.7423 ANGLE = 22163.1944 DIHED = 32332.4492 VDWAALS = -24151.9578 EEL = -190434.2919 EGB = -63090.1875 1-4 VDW = 10763.0916 1-4 EEL = 146348.1794 RESTRAINT = 0.0000 ESURF = 986.8183 minimization completed, ENE= -.56691962E+05 RMS= 0.173638E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6476E+04 1.7396E+01 1.5596E+02 C 120 BOND = 8506.0459 ANGLE = 22225.2713 DIHED = 32331.1082 VDWAALS = -24185.6713 EEL = -190096.2384 EGB = -63071.5747 1-4 VDW = 10762.8078 1-4 EEL = 146067.3901 RESTRAINT = 0.0000 ESURF = 984.4010 minimization completed, ENE= -.56476460E+05 RMS= 0.173964E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6365E+04 1.7406E+01 1.4500E+02 C 7168 BOND = 8510.8985 ANGLE = 22171.8189 DIHED = 32292.1821 VDWAALS = -24223.7393 EEL = -189828.9354 EGB = -63381.5391 1-4 VDW = 10824.5867 1-4 EEL = 146291.8128 RESTRAINT = 0.0000 ESURF = 978.3325 minimization completed, ENE= -.56364582E+05 RMS= 0.174064E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6387E+04 1.7362E+01 1.6270E+02 C 22343 BOND = 8321.5866 ANGLE = 22419.5105 DIHED = 32379.0571 VDWAALS = -24169.8894 EEL = -189953.6240 EGB = -63439.9539 1-4 VDW = 10708.7026 1-4 EEL = 146359.9474 RESTRAINT = 0.0000 ESURF = 987.8134 minimization completed, ENE= -.56386850E+05 RMS= 0.173618E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6566E+04 1.7196E+01 1.2531E+02 C 22913 BOND = 8302.9645 ANGLE = 22156.4523 DIHED = 32400.1670 VDWAALS = -24211.0804 EEL = -189977.1889 EGB = -63199.9564 1-4 VDW = 10769.5864 1-4 EEL = 146208.2841 RESTRAINT = 0.0000 ESURF = 984.6401 minimization completed, ENE= -.56566131E+05 RMS= 0.171956E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6601E+04 1.7327E+01 1.2572E+02 CD 40674 BOND = 8417.1126 ANGLE = 22155.2485 DIHED = 32429.9157 VDWAALS = -24243.8018 EEL = -190286.6404 EGB = -63115.3716 1-4 VDW = 10734.4406 1-4 EEL = 146324.5369 RESTRAINT = 0.0000 ESURF = 983.1362 minimization completed, ENE= -.56601423E+05 RMS= 0.173273E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6578E+04 1.7352E+01 1.2661E+02 CG 33390 BOND = 8419.9149 ANGLE = 22291.5611 DIHED = 32451.7656 VDWAALS = -24125.4564 EEL = -190320.2296 EGB = -63029.5447 1-4 VDW = 10620.4490 1-4 EEL = 146124.3172 RESTRAINT = 0.0000 ESURF = 988.9546 minimization completed, ENE= -.56578268E+05 RMS= 0.173518E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6565E+04 1.7385E+01 1.3571E+02 C 43927 BOND = 8443.2945 ANGLE = 22378.8751 DIHED = 32287.2221 VDWAALS = -24312.3100 EEL = -190049.6477 EGB = -63144.0772 1-4 VDW = 10628.0164 1-4 EEL = 146218.7339 RESTRAINT = 0.0000 ESURF = 984.9414 minimization completed, ENE= -.56564952E+05 RMS= 0.173851E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6520E+04 1.7377E+01 1.2832E+02 C 31883 BOND = 8472.2338 ANGLE = 22511.2284 DIHED = 32304.0030 VDWAALS = -24077.9192 EEL = -190473.5189 EGB = -62985.2914 1-4 VDW = 10603.1129 1-4 EEL = 146139.5674 RESTRAINT = 0.0000 ESURF = 986.7127 minimization completed, ENE= -.56519871E+05 RMS= 0.173775E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2858.79 ( 4.98% of Gen B) | Calc gb diag 13952.65 (24.31% of Gen B) | Calc gb off-diag 40591.40 (70.71% of Gen B) | Gen Born time 57402.84 (100.0% of Nonbo) | Nonbond force 57402.84 (100.0% of Force) | Bond/Angle/Dihedral 15.56 ( 0.03% of Force) | Force time 57418.43 (100.0% of Runmd) | Runmd Time 57418.43 (99.84% of Total) | Other 91.24 ( 0.16% of Total) | Total time 57509.80 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:32:29.336 on 10/17/2010 | Setup done at 07:32:32.636 on 10/17/2010 | Run done at 23:30:59.139 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:32:22 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.13 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.13 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6194E+04 1.7429E+01 1.2635E+02 N 32653 BOND = 8449.4786 ANGLE = 22412.8108 DIHED = 32508.2583 VDWAALS = -24167.5197 EEL = -190336.7956 EGB = -63091.2521 1-4 VDW = 10772.6779 1-4 EEL = 146273.1559 RESTRAINT = 0.0000 ESURF = 985.3947 minimization completed, ENE= -.56193791E+05 RMS= 0.174290E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6256E+04 1.7296E+01 1.2204E+02 C 10120 BOND = 8371.3875 ANGLE = 22233.0130 DIHED = 32458.5367 VDWAALS = -24112.4576 EEL = -189811.6422 EGB = -63445.7626 1-4 VDW = 10758.4164 1-4 EEL = 146301.3817 RESTRAINT = 0.0000 ESURF = 990.8644 minimization completed, ENE= -.56256263E+05 RMS= 0.172955E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6568E+04 1.7374E+01 1.2414E+02 C 38776 BOND = 8522.8704 ANGLE = 22280.4039 DIHED = 32288.4863 VDWAALS = -24196.7212 EEL = -190304.5021 EGB = -63132.9572 1-4 VDW = 10726.4726 1-4 EEL = 146255.9583 RESTRAINT = 0.0000 ESURF = 991.8274 minimization completed, ENE= -.56568162E+05 RMS= 0.173737E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6526E+04 1.7385E+01 1.3891E+02 C 38193 BOND = 8460.7439 ANGLE = 22240.4240 DIHED = 32377.9128 VDWAALS = -24185.0756 EEL = -189929.4125 EGB = -63475.1272 1-4 VDW = 10662.8988 1-4 EEL = 146325.7758 RESTRAINT = 0.0000 ESURF = 995.4237 minimization completed, ENE= -.56526436E+05 RMS= 0.173851E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6498E+04 1.7441E+01 1.3481E+02 C 21997 BOND = 8502.2491 ANGLE = 22350.6726 DIHED = 32316.1930 VDWAALS = -24060.9229 EEL = -189938.3322 EGB = -63427.2078 1-4 VDW = 10709.6288 1-4 EEL = 146056.5472 RESTRAINT = 0.0000 ESURF = 993.3478 minimization completed, ENE= -.56497824E+05 RMS= 0.174409E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6901E+04 1.7223E+01 1.1867E+02 N 40392 BOND = 8278.4334 ANGLE = 22143.6664 DIHED = 32371.2521 VDWAALS = -24184.0821 EEL = -190273.9020 EGB = -63156.5575 1-4 VDW = 10708.1187 1-4 EEL = 146222.1615 RESTRAINT = 0.0000 ESURF = 989.4496 minimization completed, ENE= -.56901460E+05 RMS= 0.172234E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6484E+04 1.7254E+01 1.3301E+02 C 1035 BOND = 8285.8924 ANGLE = 22178.1716 DIHED = 32500.9906 VDWAALS = -24090.9080 EEL = -190186.2509 EGB = -63253.2804 1-4 VDW = 10751.6598 1-4 EEL = 146340.8617 RESTRAINT = 0.0000 ESURF = 988.5456 minimization completed, ENE= -.56484317E+05 RMS= 0.172536E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6398E+04 1.7347E+01 1.4127E+02 C 16001 BOND = 8460.3599 ANGLE = 22265.9540 DIHED = 32479.7869 VDWAALS = -24109.3838 EEL = -189627.4483 EGB = -63637.2372 1-4 VDW = 10734.7233 1-4 EEL = 146045.5479 RESTRAINT = 0.0000 ESURF = 989.3451 minimization completed, ENE= -.56398352E+05 RMS= 0.173472E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6434E+04 1.7390E+01 1.3365E+02 C 218 BOND = 8355.3433 ANGLE = 22343.1682 DIHED = 32329.0882 VDWAALS = -24112.9906 EEL = -189543.2502 EGB = -63697.7939 1-4 VDW = 10713.6040 1-4 EEL = 146185.4671 RESTRAINT = 0.0000 ESURF = 993.1179 minimization completed, ENE= -.56434246E+05 RMS= 0.173899E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6592E+04 1.7330E+01 1.3461E+02 C 37641 BOND = 8313.6469 ANGLE = 22167.5057 DIHED = 32353.1199 VDWAALS = -24083.8364 EEL = -190410.5065 EGB = -63155.7187 1-4 VDW = 10812.0895 1-4 EEL = 146421.3903 RESTRAINT = 0.0000 ESURF = 990.1667 minimization completed, ENE= -.56592143E+05 RMS= 0.173296E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6467E+04 1.7300E+01 1.3343E+02 CD 21810 BOND = 8325.8090 ANGLE = 22326.3069 DIHED = 32356.8186 VDWAALS = -24148.9367 EEL = -190320.8684 EGB = -63030.9164 1-4 VDW = 10755.3382 1-4 EEL = 146278.0300 RESTRAINT = 0.0000 ESURF = 991.6299 minimization completed, ENE= -.56466789E+05 RMS= 0.172995E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6779E+04 1.7363E+01 1.3734E+02 C 2514 BOND = 8558.6644 ANGLE = 22284.9548 DIHED = 32282.6992 VDWAALS = -24262.1775 EEL = -189618.7995 EGB = -63728.9992 1-4 VDW = 10569.3644 1-4 EEL = 146142.8911 RESTRAINT = 0.0000 ESURF = 992.4921 minimization completed, ENE= -.56778910E+05 RMS= 0.173630E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6662E+04 1.7316E+01 1.3588E+02 CD 6140 BOND = 8378.9684 ANGLE = 22188.9554 DIHED = 32407.1660 VDWAALS = -24123.0498 EEL = -190310.8838 EGB = -63407.2622 1-4 VDW = 10710.0302 1-4 EEL = 146496.3226 RESTRAINT = 0.0000 ESURF = 997.8469 minimization completed, ENE= -.56661906E+05 RMS= 0.173156E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6445E+04 1.7317E+01 1.3140E+02 N 10660 BOND = 8368.4429 ANGLE = 22193.7839 DIHED = 32369.5198 VDWAALS = -24049.3704 EEL = -190115.2375 EGB = -63188.9434 1-4 VDW = 10765.2745 1-4 EEL = 146220.3803 RESTRAINT = 0.0000 ESURF = 990.8753 minimization completed, ENE= -.56445275E+05 RMS= 0.173168E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6635E+04 1.7284E+01 1.1167E+02 CD 29364 BOND = 8222.8060 ANGLE = 22168.8208 DIHED = 32390.9743 VDWAALS = -24069.5974 EEL = -190059.0370 EGB = -63483.9964 1-4 VDW = 10801.1377 1-4 EEL = 146398.0830 RESTRAINT = 0.0000 ESURF = 996.0654 minimization completed, ENE= -.56634743E+05 RMS= 0.172844E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6710E+04 1.7270E+01 1.3093E+02 CD 22464 BOND = 8425.6673 ANGLE = 22111.4282 DIHED = 32425.3475 VDWAALS = -24107.5631 EEL = -190302.2341 EGB = -63188.3792 1-4 VDW = 10735.6607 1-4 EEL = 146195.9746 RESTRAINT = 0.0000 ESURF = 994.4243 minimization completed, ENE= -.56709674E+05 RMS= 0.172701E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6386E+04 1.7441E+01 1.3376E+02 C 38518 BOND = 8589.6144 ANGLE = 22185.1342 DIHED = 32500.6467 VDWAALS = -24054.0492 EEL = -190109.7361 EGB = -63419.1709 1-4 VDW = 10747.9939 1-4 EEL = 146181.2447 RESTRAINT = 0.0000 ESURF = 992.1698 minimization completed, ENE= -.56386152E+05 RMS= 0.174412E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6442E+04 1.7310E+01 1.2822E+02 C 33404 BOND = 8405.9047 ANGLE = 22323.7587 DIHED = 32484.0419 VDWAALS = -24257.0963 EEL = -190046.8576 EGB = -63244.1355 1-4 VDW = 10740.1676 1-4 EEL = 146162.3376 RESTRAINT = 0.0000 ESURF = 989.6287 minimization completed, ENE= -.56442250E+05 RMS= 0.173100E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6486E+04 1.7355E+01 1.1710E+02 C 17971 BOND = 8395.9525 ANGLE = 22283.3721 DIHED = 32465.1864 VDWAALS = -24112.9371 EEL = -190338.6623 EGB = -63199.8672 1-4 VDW = 10755.8931 1-4 EEL = 146278.7494 RESTRAINT = 0.0000 ESURF = 986.7706 minimization completed, ENE= -.56485542E+05 RMS= 0.173552E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6515E+04 1.7245E+01 1.3201E+02 CE2 26344 BOND = 8272.7998 ANGLE = 22420.1651 DIHED = 32438.8118 VDWAALS = -24201.8321 EEL = -189948.6887 EGB = -63433.4858 1-4 VDW = 10664.0694 1-4 EEL = 146280.1796 RESTRAINT = 0.0000 ESURF = 993.1285 minimization completed, ENE= -.56514852E+05 RMS= 0.172446E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6435E+04 1.7344E+01 1.3018E+02 C 37023 BOND = 8354.9469 ANGLE = 22191.1482 DIHED = 32438.3411 VDWAALS = -24161.6281 EEL = -190335.2892 EGB = -63242.0587 1-4 VDW = 10801.6977 1-4 EEL = 146529.7099 RESTRAINT = 0.0000 ESURF = 988.3224 minimization completed, ENE= -.56434810E+05 RMS= 0.173439E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6543E+04 1.7441E+01 1.4245E+02 C 3691 BOND = 8511.8894 ANGLE = 22208.8293 DIHED = 32319.2402 VDWAALS = -24182.5311 EEL = -190478.6070 EGB = -62948.3159 1-4 VDW = 10702.9924 1-4 EEL = 146330.8775 RESTRAINT = 0.0000 ESURF = 992.3947 minimization completed, ENE= -.56543231E+05 RMS= 0.174408E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6367E+04 1.7385E+01 1.3877E+02 C 25982 BOND = 8439.2069 ANGLE = 22295.5795 DIHED = 32475.2555 VDWAALS = -23947.2634 EEL = -190642.8772 EGB = -62998.8408 1-4 VDW = 10680.8285 1-4 EEL = 146335.0549 RESTRAINT = 0.0000 ESURF = 996.2477 minimization completed, ENE= -.56366808E+05 RMS= 0.173845E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6432E+04 1.7328E+01 1.3493E+02 C 3296 BOND = 8280.7775 ANGLE = 22373.4329 DIHED = 32455.9486 VDWAALS = -24190.9057 EEL = -190499.4467 EGB = -62988.9293 1-4 VDW = 10696.9972 1-4 EEL = 146451.2858 RESTRAINT = 0.0000 ESURF = 988.5949 minimization completed, ENE= -.56432245E+05 RMS= 0.173283E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6416E+04 1.7322E+01 1.2699E+02 CA 8221 BOND = 8390.3289 ANGLE = 22178.8665 DIHED = 32508.8033 VDWAALS = -24181.3492 EEL = -190349.0686 EGB = -63073.6517 1-4 VDW = 10698.3298 1-4 EEL = 146426.0226 RESTRAINT = 0.0000 ESURF = 985.5586 minimization completed, ENE= -.56416160E+05 RMS= 0.173218E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2851.01 ( 4.96% of Gen B) | Calc gb diag 13933.70 (24.25% of Gen B) | Calc gb off-diag 40684.94 (70.79% of Gen B) | Gen Born time 57469.66 (100.0% of Nonbo) | Nonbond force 57469.66 (100.0% of Force) | Bond/Angle/Dihedral 16.70 ( 0.03% of Force) | Force time 57486.38 (100.0% of Runmd) | Runmd Time 57486.38 (99.85% of Total) | Other 87.36 ( 0.15% of Total) | Total time 57573.87 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:32:22.464 on 10/17/2010 | Setup done at 07:32:25.742 on 10/17/2010 | Run done at 23:31:56.336 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:32:16 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.12 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.12 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6476E+04 1.7362E+01 1.3486E+02 CG 44534 BOND = 8396.4830 ANGLE = 22217.3866 DIHED = 32486.9123 VDWAALS = -24162.1631 EEL = -190150.3958 EGB = -63288.5782 1-4 VDW = 10727.6958 1-4 EEL = 146307.6041 RESTRAINT = 0.0000 ESURF = 989.2460 minimization completed, ENE= -.56475809E+05 RMS= 0.173617E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6675E+04 1.7338E+01 1.4053E+02 C 34351 BOND = 8346.3468 ANGLE = 22330.7623 DIHED = 32298.8236 VDWAALS = -24080.6324 EEL = -190255.8888 EGB = -63246.5394 1-4 VDW = 10699.3137 1-4 EEL = 146240.9889 RESTRAINT = 0.0000 ESURF = 992.2391 minimization completed, ENE= -.56674586E+05 RMS= 0.173380E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6760E+04 1.7268E+01 1.2799E+02 CZ 38449 BOND = 8263.5658 ANGLE = 22187.9233 DIHED = 32370.9666 VDWAALS = -23987.1433 EEL = -190326.8058 EGB = -63357.3280 1-4 VDW = 10693.9004 1-4 EEL = 146406.4244 RESTRAINT = 0.0000 ESURF = 988.2358 minimization completed, ENE= -.56760261E+05 RMS= 0.172683E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6193E+04 1.7258E+01 1.7778E+02 CD 18181 BOND = 8308.8169 ANGLE = 22360.8455 DIHED = 32434.7924 VDWAALS = -24082.9869 EEL = -190112.1938 EGB = -63287.1698 1-4 VDW = 10808.6559 1-4 EEL = 146388.3345 RESTRAINT = 0.0000 ESURF = 988.0981 minimization completed, ENE= -.56192807E+05 RMS= 0.172582E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6528E+04 1.7334E+01 1.2188E+02 CD 32289 BOND = 8401.3210 ANGLE = 22161.7329 DIHED = 32408.4327 VDWAALS = -23920.6705 EEL = -190452.1778 EGB = -63102.3384 1-4 VDW = 10721.8728 1-4 EEL = 146257.5338 RESTRAINT = 0.0000 ESURF = 996.1703 minimization completed, ENE= -.56528123E+05 RMS= 0.173339E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6387E+04 1.7309E+01 1.3627E+02 C 14048 BOND = 8312.7296 ANGLE = 22442.5019 DIHED = 32433.5535 VDWAALS = -24290.1388 EEL = -190173.3978 EGB = -63402.5689 1-4 VDW = 10779.4697 1-4 EEL = 146517.4935 RESTRAINT = 0.0000 ESURF = 993.2266 minimization completed, ENE= -.56387131E+05 RMS= 0.173089E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6630E+04 1.7207E+01 1.3688E+02 C 39967 BOND = 8319.8059 ANGLE = 22144.5215 DIHED = 32371.4067 VDWAALS = -24108.3519 EEL = -190713.8947 EGB = -62700.5928 1-4 VDW = 10723.2828 1-4 EEL = 146340.7018 RESTRAINT = 0.0000 ESURF = 993.2074 minimization completed, ENE= -.56629913E+05 RMS= 0.172067E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6497E+04 1.7339E+01 1.1388E+02 C 12498 BOND = 8456.4615 ANGLE = 22265.2630 DIHED = 32434.8668 VDWAALS = -24084.4444 EEL = -190474.7130 EGB = -63062.7168 1-4 VDW = 10732.7650 1-4 EEL = 146238.9266 RESTRAINT = 0.0000 ESURF = 996.8902 minimization completed, ENE= -.56496701E+05 RMS= 0.173385E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6553E+04 1.7298E+01 1.3383E+02 C 2660 BOND = 8384.7311 ANGLE = 22293.4208 DIHED = 32320.6994 VDWAALS = -24020.9726 EEL = -189801.9884 EGB = -63593.1489 1-4 VDW = 10675.4866 1-4 EEL = 146188.2913 RESTRAINT = 0.0000 ESURF = 1000.0062 minimization completed, ENE= -.56553475E+05 RMS= 0.172984E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6612E+04 1.7384E+01 1.2032E+02 C 36384 BOND = 8381.6288 ANGLE = 22211.5846 DIHED = 32339.5424 VDWAALS = -23955.5099 EEL = -190140.9224 EGB = -63544.0332 1-4 VDW = 10711.2845 1-4 EEL = 146381.0879 RESTRAINT = 0.0000 ESURF = 1003.1353 minimization completed, ENE= -.56612202E+05 RMS= 0.173838E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6458E+04 1.7331E+01 1.3330E+02 CZ 28917 BOND = 8419.8726 ANGLE = 22323.3612 DIHED = 32430.0778 VDWAALS = -24109.1892 EEL = -190166.9412 EGB = -63604.1939 1-4 VDW = 10752.2079 1-4 EEL = 146497.9376 RESTRAINT = 0.0000 ESURF = 999.0802 minimization completed, ENE= -.56457787E+05 RMS= 0.173309E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6321E+04 1.7269E+01 1.3211E+02 CZ 18635 BOND = 8350.8045 ANGLE = 22446.6649 DIHED = 32479.4212 VDWAALS = -23942.3106 EEL = -190030.4906 EGB = -63590.6282 1-4 VDW = 10673.0324 1-4 EEL = 146289.9695 RESTRAINT = 0.0000 ESURF = 1002.4193 minimization completed, ENE= -.56321118E+05 RMS= 0.172694E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6687E+04 1.7279E+01 1.3014E+02 C 22121 BOND = 8291.4774 ANGLE = 22250.9733 DIHED = 32379.2304 VDWAALS = -24062.7933 EEL = -190140.6726 EGB = -63598.6641 1-4 VDW = 10722.8477 1-4 EEL = 146470.5439 RESTRAINT = 0.0000 ESURF = 1000.0555 minimization completed, ENE= -.56687002E+05 RMS= 0.172787E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6640E+04 1.7236E+01 1.2736E+02 CD 42310 BOND = 8341.5274 ANGLE = 22232.1747 DIHED = 32372.9580 VDWAALS = -24044.9470 EEL = -189485.7575 EGB = -63993.0310 1-4 VDW = 10686.8533 1-4 EEL = 146248.1370 RESTRAINT = 0.0000 ESURF = 1002.4248 minimization completed, ENE= -.56639660E+05 RMS= 0.172356E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6675E+04 1.7363E+01 1.3536E+02 C 6401 BOND = 8403.5515 ANGLE = 22108.8673 DIHED = 32467.8526 VDWAALS = -24161.5366 EEL = -189799.3598 EGB = -63756.4749 1-4 VDW = 10683.3110 1-4 EEL = 146379.0223 RESTRAINT = 0.0000 ESURF = 999.7391 minimization completed, ENE= -.56675028E+05 RMS= 0.173632E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6439E+04 1.7237E+01 1.3210E+02 N 24026 BOND = 8325.0496 ANGLE = 22269.1078 DIHED = 32433.1581 VDWAALS = -24091.3531 EEL = -190321.0024 EGB = -63341.3069 1-4 VDW = 10788.9554 1-4 EEL = 146498.0583 RESTRAINT = 0.0000 ESURF = 1000.0714 minimization completed, ENE= -.56439262E+05 RMS= 0.172367E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6425E+04 1.7313E+01 1.2747E+02 C 2855 BOND = 8343.5893 ANGLE = 22384.0983 DIHED = 32405.1755 VDWAALS = -24101.1217 EEL = -189866.1118 EGB = -63649.8403 1-4 VDW = 10716.3527 1-4 EEL = 146341.3625 RESTRAINT = 0.0000 ESURF = 1001.5474 minimization completed, ENE= -.56424948E+05 RMS= 0.173130E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6389E+04 1.7347E+01 1.1637E+02 C 42167 BOND = 8460.2065 ANGLE = 22216.4969 DIHED = 32434.6222 VDWAALS = -24032.8743 EEL = -190012.9923 EGB = -63471.1746 1-4 VDW = 10770.7336 1-4 EEL = 146248.6882 RESTRAINT = 0.0000 ESURF = 997.5133 minimization completed, ENE= -.56388781E+05 RMS= 0.173472E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6566E+04 1.7281E+01 1.2817E+02 C 37483 BOND = 8249.9625 ANGLE = 22325.6211 DIHED = 32426.0865 VDWAALS = -24033.0470 EEL = -190312.1195 EGB = -63466.0821 1-4 VDW = 10762.8017 1-4 EEL = 146478.7229 RESTRAINT = 0.0000 ESURF = 1002.4842 minimization completed, ENE= -.56565570E+05 RMS= 0.172813E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6378E+04 1.7332E+01 1.4082E+02 C 41852 BOND = 8315.6975 ANGLE = 22312.9971 DIHED = 32503.7305 VDWAALS = -24080.7193 EEL = -190051.1734 EGB = -63520.9306 1-4 VDW = 10744.3069 1-4 EEL = 146402.1110 RESTRAINT = 0.0000 ESURF = 996.1320 minimization completed, ENE= -.56377848E+05 RMS= 0.173315E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6379E+04 1.7298E+01 1.2887E+02 C 33877 BOND = 8395.4885 ANGLE = 22303.8300 DIHED = 32447.4467 VDWAALS = -24181.2464 EEL = -190060.7499 EGB = -63373.0537 1-4 VDW = 10769.7031 1-4 EEL = 146324.7554 RESTRAINT = 0.0000 ESURF = 994.5825 minimization completed, ENE= -.56379244E+05 RMS= 0.172981E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6978E+04 1.7165E+01 1.3336E+02 C 2514 BOND = 8191.0974 ANGLE = 22175.9202 DIHED = 32440.9080 VDWAALS = -24132.2375 EEL = -189738.4212 EGB = -63838.7667 1-4 VDW = 10674.9200 1-4 EEL = 146253.0456 RESTRAINT = 0.0000 ESURF = 995.8488 minimization completed, ENE= -.56977685E+05 RMS= 0.171649E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6537E+04 1.7340E+01 1.4392E+02 CG 7071 BOND = 8421.1950 ANGLE = 22206.2810 DIHED = 32386.8629 VDWAALS = -23962.8213 EEL = -190532.1472 EGB = -63137.7695 1-4 VDW = 10764.2412 1-4 EEL = 146321.4913 RESTRAINT = 0.0000 ESURF = 995.7135 minimization completed, ENE= -.56536953E+05 RMS= 0.173403E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6592E+04 1.7399E+01 1.3350E+02 C 46115 BOND = 8556.5640 ANGLE = 22187.1625 DIHED = 32337.8020 VDWAALS = -24148.8272 EEL = -189677.6096 EGB = -63608.2137 1-4 VDW = 10696.5731 1-4 EEL = 146074.1546 RESTRAINT = 0.0000 ESURF = 990.3464 minimization completed, ENE= -.56592048E+05 RMS= 0.173993E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6572E+04 1.7352E+01 1.2286E+02 C 37960 BOND = 8425.0008 ANGLE = 22303.7134 DIHED = 32398.1668 VDWAALS = -24107.0538 EEL = -190354.6262 EGB = -63225.9604 1-4 VDW = 10721.9733 1-4 EEL = 146275.1122 RESTRAINT = 0.0000 ESURF = 991.5841 minimization completed, ENE= -.56572090E+05 RMS= 0.173524E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2837.37 ( 4.95% of Gen B) | Calc gb diag 13908.91 (24.25% of Gen B) | Calc gb off-diag 40615.56 (70.81% of Gen B) | Gen Born time 57361.85 (100.0% of Nonbo) | Nonbond force 57361.85 (100.0% of Force) | Bond/Angle/Dihedral 16.89 ( 0.03% of Force) | Force time 57378.77 (100.0% of Runmd) | Runmd Time 57378.77 (99.85% of Total) | Other 88.57 ( 0.15% of Total) | Total time 57467.47 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:32:16.294 on 10/17/2010 | Setup done at 07:32:18.736 on 10/17/2010 | Run done at 23:30:03.763 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:32:10 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.11 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.11 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6393E+04 1.7317E+01 1.4047E+02 N 46345 BOND = 8487.8966 ANGLE = 22291.3889 DIHED = 32375.5091 VDWAALS = -24155.0149 EEL = -190445.5859 EGB = -62852.9814 1-4 VDW = 10721.9040 1-4 EEL = 146198.5451 RESTRAINT = 0.0000 ESURF = 985.5145 minimization completed, ENE= -.56392824E+05 RMS= 0.173175E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6369E+04 1.7394E+01 1.4201E+02 C 31618 BOND = 8566.4386 ANGLE = 22252.2824 DIHED = 32350.7747 VDWAALS = -24081.9169 EEL = -190438.1086 EGB = -63066.8076 1-4 VDW = 10644.1465 1-4 EEL = 146410.6787 RESTRAINT = 0.0000 ESURF = 993.1435 minimization completed, ENE= -.56369369E+05 RMS= 0.173944E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6410E+04 1.7293E+01 1.1557E+02 C 42272 BOND = 8347.7398 ANGLE = 22259.2175 DIHED = 32390.0083 VDWAALS = -24037.1907 EEL = -190305.2565 EGB = -63100.1944 1-4 VDW = 10768.5782 1-4 EEL = 146273.8335 RESTRAINT = 0.0000 ESURF = 993.5749 minimization completed, ENE= -.56409689E+05 RMS= 0.172935E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6480E+04 1.7260E+01 1.1538E+02 C 331 BOND = 8261.8229 ANGLE = 22235.1761 DIHED = 32398.5156 VDWAALS = -24114.7784 EEL = -190228.3788 EGB = -62998.3482 1-4 VDW = 10720.5287 1-4 EEL = 146257.4453 RESTRAINT = 0.0000 ESURF = 987.6756 minimization completed, ENE= -.56480341E+05 RMS= 0.172598E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6454E+04 1.7354E+01 1.3171E+02 CA 46161 BOND = 8354.0945 ANGLE = 22376.5032 DIHED = 32510.4557 VDWAALS = -24090.0471 EEL = -190329.6390 EGB = -63141.7393 1-4 VDW = 10709.3486 1-4 EEL = 146161.5183 RESTRAINT = 0.0000 ESURF = 995.2716 minimization completed, ENE= -.56454234E+05 RMS= 0.173536E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6457E+04 1.7417E+01 1.3134E+02 C 17689 BOND = 8446.0670 ANGLE = 22188.4879 DIHED = 32365.4962 VDWAALS = -24018.1595 EEL = -190397.5473 EGB = -62927.6599 1-4 VDW = 10727.0783 1-4 EEL = 146164.7827 RESTRAINT = 0.0000 ESURF = 994.5790 minimization completed, ENE= -.56456875E+05 RMS= 0.174167E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6196E+04 1.7499E+01 1.4435E+02 N 41698 BOND = 8487.0016 ANGLE = 22345.1169 DIHED = 32408.8608 VDWAALS = -24160.2725 EEL = -190393.5883 EGB = -62825.4288 1-4 VDW = 10726.9538 1-4 EEL = 146224.1306 RESTRAINT = 0.0000 ESURF = 990.9634 minimization completed, ENE= -.56196263E+05 RMS= 0.174993E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6398E+04 1.7371E+01 1.3158E+02 C 41776 BOND = 8395.6873 ANGLE = 22388.1971 DIHED = 32385.8803 VDWAALS = -24140.9112 EEL = -190438.4916 EGB = -62808.3998 1-4 VDW = 10774.4612 1-4 EEL = 146053.4780 RESTRAINT = 0.0000 ESURF = 991.7098 minimization completed, ENE= -.56398389E+05 RMS= 0.173711E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6441E+04 1.7380E+01 1.2911E+02 CD 18488 BOND = 8431.1524 ANGLE = 22345.3913 DIHED = 32377.0070 VDWAALS = -24126.3402 EEL = -190490.0457 EGB = -62865.6206 1-4 VDW = 10763.4532 1-4 EEL = 146132.8473 RESTRAINT = 0.0000 ESURF = 990.9381 minimization completed, ENE= -.56441217E+05 RMS= 0.173797E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6203E+04 1.7461E+01 1.2776E+02 CG 15980 BOND = 8523.6304 ANGLE = 22406.8686 DIHED = 32440.3260 VDWAALS = -24180.8573 EEL = -189858.3154 EGB = -63297.7648 1-4 VDW = 10732.6583 1-4 EEL = 146038.3778 RESTRAINT = 0.0000 ESURF = 992.2788 minimization completed, ENE= -.56202798E+05 RMS= 0.174611E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6215E+04 1.7377E+01 1.4829E+02 C 8976 BOND = 8515.7915 ANGLE = 22316.4215 DIHED = 32354.1529 VDWAALS = -24099.1179 EEL = -189767.4222 EGB = -63368.9531 1-4 VDW = 10691.6551 1-4 EEL = 146150.8935 RESTRAINT = 0.0000 ESURF = 991.4368 minimization completed, ENE= -.56215142E+05 RMS= 0.173773E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6521E+04 1.7355E+01 1.2924E+02 C 34832 BOND = 8409.1399 ANGLE = 22194.5098 DIHED = 32359.7100 VDWAALS = -24081.1996 EEL = -189615.9992 EGB = -63550.9042 1-4 VDW = 10700.6929 1-4 EEL = 146068.5138 RESTRAINT = 0.0000 ESURF = 994.3270 minimization completed, ENE= -.56521210E+05 RMS= 0.173549E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6519E+04 1.7266E+01 1.2829E+02 CG 35103 BOND = 8294.7060 ANGLE = 22309.4725 DIHED = 32339.9325 VDWAALS = -24211.5526 EEL = -189845.4243 EGB = -63264.7115 1-4 VDW = 10684.3742 1-4 EEL = 146187.4124 RESTRAINT = 0.0000 ESURF = 986.9415 minimization completed, ENE= -.56518849E+05 RMS= 0.172655E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6246E+04 1.7427E+01 1.2835E+02 CG 27702 BOND = 8380.2372 ANGLE = 22438.5257 DIHED = 32419.0472 VDWAALS = -24083.6791 EEL = -190192.2010 EGB = -63242.8499 1-4 VDW = 10791.2867 1-4 EEL = 146252.4668 RESTRAINT = 0.0000 ESURF = 991.1748 minimization completed, ENE= -.56245992E+05 RMS= 0.174265E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6201E+04 1.7379E+01 1.4823E+02 CD 13640 BOND = 8358.1252 ANGLE = 22489.3219 DIHED = 32441.6602 VDWAALS = -24207.5090 EEL = -189669.8922 EGB = -63569.7174 1-4 VDW = 10752.1477 1-4 EEL = 146218.2468 RESTRAINT = 0.0000 ESURF = 986.5137 minimization completed, ENE= -.56201103E+05 RMS= 0.173787E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6178E+04 1.7321E+01 1.2468E+02 C 7741 BOND = 8371.7855 ANGLE = 22418.6462 DIHED = 32507.0180 VDWAALS = -24103.3011 EEL = -189728.9997 EGB = -63328.9867 1-4 VDW = 10700.5530 1-4 EEL = 145998.2937 RESTRAINT = 0.0000 ESURF = 987.2263 minimization completed, ENE= -.56177765E+05 RMS= 0.173208E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6591E+04 1.7284E+01 1.3731E+02 C 3782 BOND = 8377.0952 ANGLE = 22321.8113 DIHED = 32297.7900 VDWAALS = -23953.0541 EEL = -190472.6471 EGB = -63142.2763 1-4 VDW = 10717.1497 1-4 EEL = 146274.2605 RESTRAINT = 0.0000 ESURF = 988.6162 minimization completed, ENE= -.56591255E+05 RMS= 0.172836E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6497E+04 1.7231E+01 1.3057E+02 N 15656 BOND = 8260.4233 ANGLE = 22202.1980 DIHED = 32445.3282 VDWAALS = -24048.8528 EEL = -190416.3328 EGB = -63154.0997 1-4 VDW = 10762.9031 1-4 EEL = 146457.1500 RESTRAINT = 0.0000 ESURF = 994.6409 minimization completed, ENE= -.56496642E+05 RMS= 0.172306E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6357E+04 1.7344E+01 1.2015E+02 CE 25997 BOND = 8405.2828 ANGLE = 22402.4654 DIHED = 32418.4605 VDWAALS = -24105.0505 EEL = -190264.2934 EGB = -63070.4870 1-4 VDW = 10712.7369 1-4 EEL = 146151.2962 RESTRAINT = 0.0000 ESURF = 992.5196 minimization completed, ENE= -.56357069E+05 RMS= 0.173443E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6560E+04 1.7350E+01 1.3444E+02 C 8738 BOND = 8359.8421 ANGLE = 22256.5398 DIHED = 32454.6106 VDWAALS = -24080.2329 EEL = -189768.2749 EGB = -63784.8482 1-4 VDW = 10678.6041 1-4 EEL = 146330.0964 RESTRAINT = 0.0000 ESURF = 993.6475 minimization completed, ENE= -.56560015E+05 RMS= 0.173498E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6490E+04 1.7304E+01 1.4478E+02 C 43884 BOND = 8206.3057 ANGLE = 22436.0423 DIHED = 32533.9484 VDWAALS = -24054.4207 EEL = -190169.0995 EGB = -63514.9468 1-4 VDW = 10724.4453 1-4 EEL = 146355.3235 RESTRAINT = 0.0000 ESURF = 992.7024 minimization completed, ENE= -.56489699E+05 RMS= 0.173038E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6586E+04 1.7317E+01 1.5945E+02 CD 17169 BOND = 8406.9588 ANGLE = 22424.6009 DIHED = 32278.8670 VDWAALS = -24174.8012 EEL = -190260.8358 EGB = -63251.2584 1-4 VDW = 10711.3568 1-4 EEL = 146293.1694 RESTRAINT = 0.0000 ESURF = 985.5497 minimization completed, ENE= -.56586393E+05 RMS= 0.173171E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6644E+04 1.7237E+01 1.2787E+02 CG 24500 BOND = 8234.0253 ANGLE = 22248.1287 DIHED = 32337.7071 VDWAALS = -24004.7500 EEL = -190651.3619 EGB = -62963.5306 1-4 VDW = 10761.9142 1-4 EEL = 146404.6859 RESTRAINT = 0.0000 ESURF = 989.6454 minimization completed, ENE= -.56643536E+05 RMS= 0.172373E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6334E+04 1.7377E+01 1.3320E+02 CD 15039 BOND = 8405.8433 ANGLE = 22450.9251 DIHED = 32426.4125 VDWAALS = -24177.4611 EEL = -190159.5612 EGB = -63166.5985 1-4 VDW = 10703.3036 1-4 EEL = 146193.9023 RESTRAINT = 0.0000 ESURF = 989.1779 minimization completed, ENE= -.56334056E+05 RMS= 0.173770E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6276E+04 1.7379E+01 1.2796E+02 CD 7204 BOND = 8553.4064 ANGLE = 22366.4531 DIHED = 32423.7721 VDWAALS = -24067.9501 EEL = -190470.8413 EGB = -63031.8952 1-4 VDW = 10753.5376 1-4 EEL = 146210.2192 RESTRAINT = 0.0000 ESURF = 987.4678 minimization completed, ENE= -.56275830E+05 RMS= 0.173790E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2839.09 ( 4.91% of Gen B) | Calc gb diag 13636.91 (23.56% of Gen B) | Calc gb off-diag 41401.05 (71.53% of Gen B) | Gen Born time 57877.06 (100.0% of Nonbo) | Nonbond force 57877.06 (100.0% of Force) | Bond/Angle/Dihedral 15.54 ( 0.03% of Force) | Force time 57892.63 (100.0% of Runmd) | Runmd Time 57892.63 (99.86% of Total) | Other 83.77 ( 0.14% of Total) | Total time 57976.53 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:32:10.669 on 10/17/2010 | Setup done at 07:32:13.691 on 10/17/2010 | Run done at 23:38:27.195 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:32:04 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.10 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.10 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6670E+04 1.7228E+01 1.5833E+02 CD 8988 BOND = 8382.0778 ANGLE = 22228.2905 DIHED = 32387.1435 VDWAALS = -24218.1025 EEL = -190672.6017 EGB = -62761.3377 1-4 VDW = 10726.0615 1-4 EEL = 146271.2362 RESTRAINT = 0.0000 ESURF = 986.8012 minimization completed, ENE= -.56670431E+05 RMS= 0.172277E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6599E+04 1.7236E+01 1.2315E+02 CD 45669 BOND = 8317.0414 ANGLE = 22128.9551 DIHED = 32331.1213 VDWAALS = -24056.3725 EEL = -190666.5842 EGB = -62797.5158 1-4 VDW = 10794.9166 1-4 EEL = 146362.7626 RESTRAINT = 0.0000 ESURF = 986.2604 minimization completed, ENE= -.56599415E+05 RMS= 0.172359E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6235E+04 1.7396E+01 1.2856E+02 CD 35954 BOND = 8460.5442 ANGLE = 22545.2979 DIHED = 32326.5283 VDWAALS = -24091.2910 EEL = -190687.4171 EGB = -62924.9275 1-4 VDW = 10728.3314 1-4 EEL = 146423.3141 RESTRAINT = 0.0000 ESURF = 984.1421 minimization completed, ENE= -.56235478E+05 RMS= 0.173962E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6736E+04 1.7319E+01 1.4368E+02 C 22570 BOND = 8451.3107 ANGLE = 22198.0995 DIHED = 32309.0392 VDWAALS = -24083.3060 EEL = -190560.0469 EGB = -62922.5135 1-4 VDW = 10663.1239 1-4 EEL = 146217.4769 RESTRAINT = 0.0000 ESURF = 990.7115 minimization completed, ENE= -.56736105E+05 RMS= 0.173186E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6601E+04 1.7256E+01 1.2703E+02 C 16388 BOND = 8268.0131 ANGLE = 22255.1972 DIHED = 32410.8400 VDWAALS = -24060.3684 EEL = -190815.4294 EGB = -62763.0473 1-4 VDW = 10719.7452 1-4 EEL = 146398.0207 RESTRAINT = 0.0000 ESURF = 985.8932 minimization completed, ENE= -.56601136E+05 RMS= 0.172557E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6407E+04 1.7404E+01 1.2068E+02 C 28122 BOND = 8321.2192 ANGLE = 22389.6504 DIHED = 32419.7337 VDWAALS = -24067.9178 EEL = -190623.0909 EGB = -62854.6376 1-4 VDW = 10773.7115 1-4 EEL = 146245.5935 RESTRAINT = 0.0000 ESURF = 989.1721 minimization completed, ENE= -.56406566E+05 RMS= 0.174037E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6383E+04 1.7378E+01 1.4594E+02 C 39625 BOND = 8454.0670 ANGLE = 22478.3130 DIHED = 32356.7245 VDWAALS = -24108.2210 EEL = -190605.7700 EGB = -62904.6904 1-4 VDW = 10683.9544 1-4 EEL = 146273.1756 RESTRAINT = 0.0000 ESURF = 989.9254 minimization completed, ENE= -.56382522E+05 RMS= 0.173783E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6446E+04 1.7482E+01 1.3076E+02 C 43112 BOND = 8441.5404 ANGLE = 22491.0322 DIHED = 32403.6729 VDWAALS = -24110.5627 EEL = -190634.8269 EGB = -62813.3042 1-4 VDW = 10674.8065 1-4 EEL = 146109.5536 RESTRAINT = 0.0000 ESURF = 991.6875 minimization completed, ENE= -.56446401E+05 RMS= 0.174822E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6415E+04 1.7290E+01 1.3570E+02 C 17971 BOND = 8359.5783 ANGLE = 22310.3298 DIHED = 32396.0617 VDWAALS = -24134.8235 EEL = -190523.9173 EGB = -62675.5824 1-4 VDW = 10755.7402 1-4 EEL = 146109.5792 RESTRAINT = 0.0000 ESURF = 988.0354 minimization completed, ENE= -.56414999E+05 RMS= 0.172903E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6195E+04 1.7397E+01 1.6795E+02 CD 43869 BOND = 8284.8854 ANGLE = 22354.4351 DIHED = 32355.3089 VDWAALS = -24126.0002 EEL = -189808.6786 EGB = -63352.0113 1-4 VDW = 10818.8326 1-4 EEL = 146290.8501 RESTRAINT = 0.0000 ESURF = 987.2580 minimization completed, ENE= -.56195120E+05 RMS= 0.173972E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6603E+04 1.7317E+01 1.3652E+02 C 15609 BOND = 8465.6707 ANGLE = 22077.1355 DIHED = 32454.6858 VDWAALS = -24142.2110 EEL = -190596.3880 EGB = -62625.5335 1-4 VDW = 10692.0209 1-4 EEL = 146087.5245 RESTRAINT = 0.0000 ESURF = 984.5777 minimization completed, ENE= -.56602517E+05 RMS= 0.173170E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6468E+04 1.7243E+01 1.3663E+02 C 37944 BOND = 8328.6166 ANGLE = 22421.2740 DIHED = 32377.6418 VDWAALS = -24136.7317 EEL = -190291.5183 EGB = -62936.5556 1-4 VDW = 10703.6510 1-4 EEL = 146077.2306 RESTRAINT = 0.0000 ESURF = 988.3129 minimization completed, ENE= -.56468079E+05 RMS= 0.172431E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6206E+04 1.7343E+01 1.3656E+02 C 16388 BOND = 8466.7638 ANGLE = 22269.3489 DIHED = 32486.1543 VDWAALS = -24012.2036 EEL = -190244.7009 EGB = -63061.1683 1-4 VDW = 10703.4541 1-4 EEL = 146196.4630 RESTRAINT = 0.0000 ESURF = 989.5968 minimization completed, ENE= -.56206292E+05 RMS= 0.173431E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6370E+04 1.7359E+01 1.2335E+02 C 6885 BOND = 8427.6569 ANGLE = 22325.7129 DIHED = 32339.7441 VDWAALS = -24015.8981 EEL = -189900.9841 EGB = -63358.9892 1-4 VDW = 10641.2226 1-4 EEL = 146178.2386 RESTRAINT = 0.0000 ESURF = 993.7363 minimization completed, ENE= -.56369560E+05 RMS= 0.173586E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6468E+04 1.7389E+01 1.4767E+02 CD 5184 BOND = 8532.7433 ANGLE = 22118.5173 DIHED = 32346.5184 VDWAALS = -24131.5916 EEL = -190569.2790 EGB = -62805.6061 1-4 VDW = 10819.2965 1-4 EEL = 146228.7972 RESTRAINT = 0.0000 ESURF = 992.7212 minimization completed, ENE= -.56467883E+05 RMS= 0.173890E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6709E+04 1.7308E+01 1.2691E+02 C 44174 BOND = 8351.0930 ANGLE = 22199.4812 DIHED = 32409.5873 VDWAALS = -24091.3536 EEL = -190491.6601 EGB = -62899.1348 1-4 VDW = 10668.1920 1-4 EEL = 146155.8173 RESTRAINT = 0.0000 ESURF = 989.0734 minimization completed, ENE= -.56708904E+05 RMS= 0.173084E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6466E+04 1.7366E+01 1.3899E+02 C 27302 BOND = 8432.7877 ANGLE = 22119.9021 DIHED = 32323.9755 VDWAALS = -24080.6144 EEL = -189717.2700 EGB = -63477.5361 1-4 VDW = 10747.1665 1-4 EEL = 146195.7055 RESTRAINT = 0.0000 ESURF = 989.6875 minimization completed, ENE= -.56466196E+05 RMS= 0.173663E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6525E+04 1.7216E+01 1.2540E+02 CD 5774 BOND = 8391.7836 ANGLE = 22137.9620 DIHED = 32370.1975 VDWAALS = -24179.9327 EEL = -189700.7328 EGB = -63447.6465 1-4 VDW = 10710.2385 1-4 EEL = 146203.4576 RESTRAINT = 0.0000 ESURF = 989.1847 minimization completed, ENE= -.56525488E+05 RMS= 0.172162E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6350E+04 1.7377E+01 1.2667E+02 C 36988 BOND = 8446.0194 ANGLE = 22243.8999 DIHED = 32393.3773 VDWAALS = -24134.6140 EEL = -189759.3476 EGB = -63372.9867 1-4 VDW = 10701.0300 1-4 EEL = 146142.1258 RESTRAINT = 0.0000 ESURF = 990.7037 minimization completed, ENE= -.56349792E+05 RMS= 0.173767E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6358E+04 1.7376E+01 1.3104E+02 CG 782 BOND = 8434.9027 ANGLE = 22124.0447 DIHED = 32415.9149 VDWAALS = -24154.8034 EEL = -189761.6607 EGB = -63442.5643 1-4 VDW = 10743.5494 1-4 EEL = 146292.6853 RESTRAINT = 0.0000 ESURF = 990.3814 minimization completed, ENE= -.56357550E+05 RMS= 0.173764E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6424E+04 1.7324E+01 1.2705E+02 N 33084 BOND = 8419.7978 ANGLE = 22185.7385 DIHED = 32435.1070 VDWAALS = -24077.5230 EEL = -189698.6640 EGB = -63634.9248 1-4 VDW = 10741.6527 1-4 EEL = 146214.3807 RESTRAINT = 0.0000 ESURF = 990.0407 minimization completed, ENE= -.56424394E+05 RMS= 0.173243E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6516E+04 1.7318E+01 1.2824E+02 CD 36601 BOND = 8407.4240 ANGLE = 22236.4880 DIHED = 32274.6470 VDWAALS = -24064.7680 EEL = -190036.2824 EGB = -63370.4499 1-4 VDW = 10765.1078 1-4 EEL = 146285.2549 RESTRAINT = 0.0000 ESURF = 986.6782 minimization completed, ENE= -.56515900E+05 RMS= 0.173180E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6444E+04 1.7372E+01 1.3577E+02 C 1927 BOND = 8418.4207 ANGLE = 22302.8777 DIHED = 32324.2605 VDWAALS = -24000.4590 EEL = -190130.8028 EGB = -63196.5904 1-4 VDW = 10757.2463 1-4 EEL = 146089.4990 RESTRAINT = 0.0000 ESURF = 991.7469 minimization completed, ENE= -.56443801E+05 RMS= 0.173723E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6374E+04 1.7272E+01 1.3311E+02 C 26412 BOND = 8378.2722 ANGLE = 22313.5103 DIHED = 32382.4761 VDWAALS = -24142.0764 EEL = -190339.3504 EGB = -62914.7552 1-4 VDW = 10724.1531 1-4 EEL = 146242.9556 RESTRAINT = 0.0000 ESURF = 981.2215 minimization completed, ENE= -.56373593E+05 RMS= 0.172724E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6557E+04 1.7343E+01 1.3873E+02 CD1 34301 BOND = 8342.1082 ANGLE = 22235.7611 DIHED = 32277.1797 VDWAALS = -24053.0373 EEL = -190376.1956 EGB = -62871.8096 1-4 VDW = 10738.7517 1-4 EEL = 146157.3281 RESTRAINT = 0.0000 ESURF = 992.8200 minimization completed, ENE= -.56557094E+05 RMS= 0.173432E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2848.00 ( 4.96% of Gen B) | Calc gb diag 13949.26 (24.29% of Gen B) | Calc gb off-diag 40636.17 (70.75% of Gen B) | Gen Born time 57433.44 (100.0% of Nonbo) | Nonbond force 57433.44 (100.0% of Force) | Bond/Angle/Dihedral 15.95 ( 0.03% of Force) | Force time 57449.42 (100.0% of Runmd) | Runmd Time 57449.42 (99.84% of Total) | Other 89.23 ( 0.16% of Total) | Total time 57538.78 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:32:04.482 on 10/17/2010 | Setup done at 07:32:08.062 on 10/17/2010 | Run done at 23:31:03.261 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:31:58 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.9 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.9 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6520E+04 1.7412E+01 1.3227E+02 C 23981 BOND = 8440.5444 ANGLE = 22315.9047 DIHED = 32271.0396 VDWAALS = -24135.1945 EEL = -190559.8202 EGB = -62940.9163 1-4 VDW = 10760.2208 1-4 EEL = 146340.7915 RESTRAINT = 0.0000 ESURF = 987.5344 minimization completed, ENE= -.56519895E+05 RMS= 0.174118E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6477E+04 1.7332E+01 1.2279E+02 C 39081 BOND = 8352.8259 ANGLE = 22420.4994 DIHED = 32379.9109 VDWAALS = -24202.8761 EEL = -190204.6395 EGB = -63041.2833 1-4 VDW = 10628.2675 1-4 EEL = 146207.4523 RESTRAINT = 0.0000 ESURF = 982.8014 minimization completed, ENE= -.56477041E+05 RMS= 0.173319E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6352E+04 1.7331E+01 1.3800E+02 CA 41041 BOND = 8452.9418 ANGLE = 22304.4497 DIHED = 32513.4718 VDWAALS = -24106.0521 EEL = -190530.1901 EGB = -63082.3280 1-4 VDW = 10723.0653 1-4 EEL = 146387.9861 RESTRAINT = 0.0000 ESURF = 984.4651 minimization completed, ENE= -.56352190E+05 RMS= 0.173314E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6267E+04 1.7359E+01 1.3549E+02 CZ 36716 BOND = 8411.4580 ANGLE = 22523.3763 DIHED = 32423.6140 VDWAALS = -24174.0475 EEL = -190748.8003 EGB = -62553.8728 1-4 VDW = 10668.3306 1-4 EEL = 146204.1904 RESTRAINT = 0.0000 ESURF = 978.7717 minimization completed, ENE= -.56266980E+05 RMS= 0.173593E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6668E+04 1.7280E+01 1.2991E+02 CG 40423 BOND = 8406.9496 ANGLE = 22249.9954 DIHED = 32278.3149 VDWAALS = -24067.6187 EEL = -190398.6166 EGB = -63027.4315 1-4 VDW = 10698.8615 1-4 EEL = 146206.6587 RESTRAINT = 0.0000 ESURF = 985.1386 minimization completed, ENE= -.56667748E+05 RMS= 0.172804E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6587E+04 1.7309E+01 1.3085E+02 N 6675 BOND = 8383.1234 ANGLE = 22006.7215 DIHED = 32370.4323 VDWAALS = -24103.2324 EEL = -190557.3229 EGB = -62785.2109 1-4 VDW = 10789.5513 1-4 EEL = 146325.8907 RESTRAINT = 0.0000 ESURF = 983.3102 minimization completed, ENE= -.56586737E+05 RMS= 0.173087E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6363E+04 1.7353E+01 1.3320E+02 C 37944 BOND = 8462.0593 ANGLE = 22385.9576 DIHED = 32300.4097 VDWAALS = -24217.9937 EEL = -190142.9551 EGB = -63046.7112 1-4 VDW = 10710.7182 1-4 EEL = 146203.6924 RESTRAINT = 0.0000 ESURF = 981.5233 minimization completed, ENE= -.56363300E+05 RMS= 0.173526E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6749E+04 1.7250E+01 1.4250E+02 CD 41686 BOND = 8339.6956 ANGLE = 22091.5543 DIHED = 32360.3179 VDWAALS = -24198.9755 EEL = -190306.5366 EGB = -63092.8000 1-4 VDW = 10718.6236 1-4 EEL = 146353.5059 RESTRAINT = 0.0000 ESURF = 985.7393 minimization completed, ENE= -.56748875E+05 RMS= 0.172502E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6701E+04 1.7327E+01 1.3074E+02 C 33202 BOND = 8310.4791 ANGLE = 22239.5872 DIHED = 32423.4375 VDWAALS = -24194.4613 EEL = -190266.0388 EGB = -62989.0219 1-4 VDW = 10660.8970 1-4 EEL = 146122.6103 RESTRAINT = 0.0000 ESURF = 991.3718 minimization completed, ENE= -.56701139E+05 RMS= 0.173271E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6383E+04 1.7443E+01 1.1346E+02 C 24646 BOND = 8461.7636 ANGLE = 22300.2854 DIHED = 32420.6690 VDWAALS = -24054.3283 EEL = -190415.9197 EGB = -63084.6290 1-4 VDW = 10744.7502 1-4 EEL = 146260.1827 RESTRAINT = 0.0000 ESURF = 983.9016 minimization completed, ENE= -.56383324E+05 RMS= 0.174429E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6442E+04 1.7361E+01 1.2764E+02 C 39625 BOND = 8472.3000 ANGLE = 22146.4518 DIHED = 32387.9577 VDWAALS = -24058.1852 EEL = -190058.1823 EGB = -63171.6791 1-4 VDW = 10754.3039 1-4 EEL = 146099.8998 RESTRAINT = 0.0000 ESURF = 985.5915 minimization completed, ENE= -.56441542E+05 RMS= 0.173614E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6550E+04 1.7320E+01 1.3197E+02 CG 27437 BOND = 8324.4746 ANGLE = 22241.6149 DIHED = 32248.3083 VDWAALS = -24099.5824 EEL = -190391.9733 EGB = -63177.1359 1-4 VDW = 10737.8470 1-4 EEL = 146580.4144 RESTRAINT = 0.0000 ESURF = 986.5222 minimization completed, ENE= -.56549510E+05 RMS= 0.173198E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6476E+04 1.7284E+01 1.1629E+02 C 5044 BOND = 8342.5549 ANGLE = 22357.1350 DIHED = 32484.9778 VDWAALS = -24137.3188 EEL = -190258.8667 EGB = -63166.8859 1-4 VDW = 10699.9221 1-4 EEL = 146215.5576 RESTRAINT = 0.0000 ESURF = 986.6491 minimization completed, ENE= -.56476275E+05 RMS= 0.172845E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6265E+04 1.7384E+01 1.2652E+02 C 10255 BOND = 8410.1058 ANGLE = 22374.4137 DIHED = 32422.4361 VDWAALS = -24153.9283 EEL = -190040.7289 EGB = -63238.2278 1-4 VDW = 10756.6704 1-4 EEL = 146223.3929 RESTRAINT = 0.0000 ESURF = 980.4338 minimization completed, ENE= -.56265432E+05 RMS= 0.173843E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6482E+04 1.7414E+01 1.2935E+02 CD 20982 BOND = 8458.0156 ANGLE = 22092.5768 DIHED = 32496.1969 VDWAALS = -24063.3305 EEL = -190258.1706 EGB = -63103.2146 1-4 VDW = 10722.3116 1-4 EEL = 146191.6624 RESTRAINT = 0.0000 ESURF = 982.4412 minimization completed, ENE= -.56481511E+05 RMS= 0.174140E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6560E+04 1.7223E+01 1.2898E+02 CZ 44551 BOND = 8410.5395 ANGLE = 22192.8754 DIHED = 32260.2430 VDWAALS = -24235.7800 EEL = -189985.4776 EGB = -63205.7646 1-4 VDW = 10701.0257 1-4 EEL = 146319.9871 RESTRAINT = 0.0000 ESURF = 982.2198 minimization completed, ENE= -.56560132E+05 RMS= 0.172226E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6719E+04 1.7292E+01 1.1924E+02 C 26612 BOND = 8276.3962 ANGLE = 22134.4410 DIHED = 32366.7825 VDWAALS = -24191.9884 EEL = -190431.7754 EGB = -62936.4990 1-4 VDW = 10755.7925 1-4 EEL = 146323.6428 RESTRAINT = 0.0000 ESURF = 984.4779 minimization completed, ENE= -.56718730E+05 RMS= 0.172923E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6916E+04 1.7193E+01 1.2415E+02 C 37553 BOND = 8342.6824 ANGLE = 22167.8138 DIHED = 32418.3562 VDWAALS = -24220.9548 EEL = -190551.6326 EGB = -62859.4061 1-4 VDW = 10628.7441 1-4 EEL = 146170.1099 RESTRAINT = 0.0000 ESURF = 988.5556 minimization completed, ENE= -.56915732E+05 RMS= 0.171929E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6653E+04 1.7308E+01 1.1308E+02 C 18207 BOND = 8209.8478 ANGLE = 22244.1693 DIHED = 32451.1237 VDWAALS = -24191.2033 EEL = -191033.9338 EGB = -62293.7046 1-4 VDW = 10777.1760 1-4 EEL = 146199.7593 RESTRAINT = 0.0000 ESURF = 983.3102 minimization completed, ENE= -.56653455E+05 RMS= 0.173079E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6565E+04 1.7265E+01 1.6259E+02 C 33089 BOND = 8292.9344 ANGLE = 22330.9927 DIHED = 32554.4549 VDWAALS = -24134.2472 EEL = -190977.4811 EGB = -62411.1173 1-4 VDW = 10645.8436 1-4 EEL = 146146.7730 RESTRAINT = 0.0000 ESURF = 986.7079 minimization completed, ENE= -.56565139E+05 RMS= 0.172645E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6403E+04 1.7203E+01 1.2437E+02 C 35979 BOND = 8291.4939 ANGLE = 22361.3465 DIHED = 32437.8660 VDWAALS = -23976.0648 EEL = -191002.7738 EGB = -62449.8608 1-4 VDW = 10749.1972 1-4 EEL = 146200.2277 RESTRAINT = 0.0000 ESURF = 985.8970 minimization completed, ENE= -.56402671E+05 RMS= 0.172029E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6656E+04 1.7291E+01 1.2507E+02 CZ 27746 BOND = 8305.9605 ANGLE = 22104.8966 DIHED = 32446.4963 VDWAALS = -23929.6041 EEL = -191572.3732 EGB = -62187.3567 1-4 VDW = 10776.2811 1-4 EEL = 146413.3100 RESTRAINT = 0.0000 ESURF = 985.9463 minimization completed, ENE= -.56656443E+05 RMS= 0.172909E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6408E+04 1.7349E+01 1.2833E+02 C 28667 BOND = 8364.1118 ANGLE = 22257.5318 DIHED = 32450.1576 VDWAALS = -24097.8602 EEL = -190332.8671 EGB = -62973.0574 1-4 VDW = 10668.6420 1-4 EEL = 146267.5818 RESTRAINT = 0.0000 ESURF = 988.1698 minimization completed, ENE= -.56407590E+05 RMS= 0.173492E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6582E+04 1.7385E+01 1.3997E+02 C 23548 BOND = 8395.7099 ANGLE = 22149.2919 DIHED = 32448.8019 VDWAALS = -24086.4297 EEL = -191232.3184 EGB = -62286.4738 1-4 VDW = 10742.2156 1-4 EEL = 146297.2190 RESTRAINT = 0.0000 ESURF = 989.4991 minimization completed, ENE= -.56582484E+05 RMS= 0.173854E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6677E+04 1.7283E+01 1.3512E+02 CA 18173 BOND = 8332.3167 ANGLE = 22109.4941 DIHED = 32403.9192 VDWAALS = -24106.5644 EEL = -191014.7268 EGB = -62515.9657 1-4 VDW = 10713.4645 1-4 EEL = 146416.8070 RESTRAINT = 0.0000 ESURF = 984.5652 minimization completed, ENE= -.56676690E+05 RMS= 0.172834E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2845.36 ( 4.96% of Gen B) | Calc gb diag 13957.58 (24.31% of Gen B) | Calc gb off-diag 40609.45 (70.73% of Gen B) | Gen Born time 57412.40 (100.0% of Nonbo) | Nonbond force 57412.40 (100.0% of Force) | Bond/Angle/Dihedral 16.95 ( 0.03% of Force) | Force time 57429.68 (100.0% of Runmd) | Runmd Time 57429.68 (99.84% of Total) | Other 94.09 ( 0.16% of Total) | Total time 57523.91 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:31:58.380 on 10/17/2010 | Setup done at 07:32:01.137 on 10/17/2010 | Run done at 23:30:42.287 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:31:51 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.8 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.8 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6750E+04 1.7318E+01 1.5346E+02 N 30651 BOND = 8528.5506 ANGLE = 21961.2271 DIHED = 32263.1516 VDWAALS = -24232.1794 EEL = -190105.6716 EGB = -63135.5538 1-4 VDW = 10740.2579 1-4 EEL = 146237.0472 RESTRAINT = 0.0000 ESURF = 993.3627 minimization completed, ENE= -.56749808E+05 RMS= 0.173180E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6189E+04 1.7287E+01 1.1870E+02 C 2041 BOND = 8452.6717 ANGLE = 22528.6333 DIHED = 32285.2395 VDWAALS = -24112.8487 EEL = -190012.5917 EGB = -63363.0354 1-4 VDW = 10705.5564 1-4 EEL = 146336.7274 RESTRAINT = 0.0000 ESURF = 991.0830 minimization completed, ENE= -.56188564E+05 RMS= 0.172867E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6355E+04 1.7332E+01 1.2812E+02 C 14653 BOND = 8413.8665 ANGLE = 22323.4561 DIHED = 32356.0159 VDWAALS = -24108.0099 EEL = -189973.1617 EGB = -63344.7614 1-4 VDW = 10706.7690 1-4 EEL = 146276.1818 RESTRAINT = 0.0000 ESURF = 994.6122 minimization completed, ENE= -.56355032E+05 RMS= 0.173322E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6473E+04 1.7297E+01 1.3078E+02 CD 21795 BOND = 8404.6003 ANGLE = 22043.4260 DIHED = 32484.1557 VDWAALS = -24124.9399 EEL = -190371.0446 EGB = -63053.9023 1-4 VDW = 10752.7652 1-4 EEL = 146402.4295 RESTRAINT = 0.0000 ESURF = 989.7204 minimization completed, ENE= -.56472790E+05 RMS= 0.172973E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6313E+04 1.7400E+01 1.3187E+02 N 7012 BOND = 8462.2119 ANGLE = 22230.3614 DIHED = 32287.9739 VDWAALS = -24021.8908 EEL = -190172.6628 EGB = -63115.7503 1-4 VDW = 10711.1606 1-4 EEL = 146308.4285 RESTRAINT = 0.0000 ESURF = 996.6839 minimization completed, ENE= -.56313484E+05 RMS= 0.174003E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6249E+04 1.7421E+01 1.5152E+02 C 29534 BOND = 8373.2571 ANGLE = 22386.0699 DIHED = 32471.6430 VDWAALS = -24014.4431 EEL = -190192.6315 EGB = -63179.5504 1-4 VDW = 10738.8253 1-4 EEL = 146172.4538 RESTRAINT = 0.0000 ESURF = 994.9882 minimization completed, ENE= -.56249388E+05 RMS= 0.174208E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6567E+04 1.7290E+01 1.4877E+02 C 13828 BOND = 8449.7209 ANGLE = 22186.2956 DIHED = 32412.4125 VDWAALS = -24138.7133 EEL = -190451.3157 EGB = -62979.7777 1-4 VDW = 10687.3390 1-4 EEL = 146273.8226 RESTRAINT = 0.0000 ESURF = 993.1500 minimization completed, ENE= -.56567066E+05 RMS= 0.172897E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6446E+04 1.7336E+01 1.2860E+02 C 1290 BOND = 8464.9288 ANGLE = 22202.6359 DIHED = 32349.7817 VDWAALS = -24035.8431 EEL = -190376.5606 EGB = -62951.8688 1-4 VDW = 10698.5803 1-4 EEL = 146209.1674 RESTRAINT = 0.0000 ESURF = 993.1293 minimization completed, ENE= -.56446049E+05 RMS= 0.173356E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6418E+04 1.7368E+01 1.2116E+02 C 21554 BOND = 8427.5467 ANGLE = 22148.8608 DIHED = 32321.9474 VDWAALS = -24165.3761 EEL = -190377.8320 EGB = -62908.0849 1-4 VDW = 10792.7969 1-4 EEL = 146353.0248 RESTRAINT = 0.0000 ESURF = 989.1126 minimization completed, ENE= -.56418004E+05 RMS= 0.173685E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6296E+04 1.7342E+01 1.4193E+02 C 5940 BOND = 8430.2495 ANGLE = 22199.8884 DIHED = 32446.3638 VDWAALS = -24129.4963 EEL = -189900.9585 EGB = -63484.5766 1-4 VDW = 10740.0740 1-4 EEL = 146408.9495 RESTRAINT = 0.0000 ESURF = 993.0575 minimization completed, ENE= -.56296449E+05 RMS= 0.173417E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6278E+04 1.7283E+01 1.2893E+02 CG 28897 BOND = 8342.0423 ANGLE = 22431.6880 DIHED = 32363.4765 VDWAALS = -24158.7571 EEL = -190270.1741 EGB = -62875.9965 1-4 VDW = 10700.7529 1-4 EEL = 146198.6390 RESTRAINT = 0.0000 ESURF = 990.5167 minimization completed, ENE= -.56277812E+05 RMS= 0.172827E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6521E+04 1.7307E+01 1.2829E+02 C 37546 BOND = 8354.4141 ANGLE = 22117.1660 DIHED = 32429.8298 VDWAALS = -24094.4048 EEL = -190279.6859 EGB = -63092.7471 1-4 VDW = 10803.1686 1-4 EEL = 146256.3498 RESTRAINT = 0.0000 ESURF = 984.9504 minimization completed, ENE= -.56520959E+05 RMS= 0.173071E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6628E+04 1.7230E+01 1.2458E+02 N 18927 BOND = 8227.1031 ANGLE = 22224.3619 DIHED = 32392.7130 VDWAALS = -24178.6475 EEL = -190672.5728 EGB = -62666.7480 1-4 VDW = 10750.1238 1-4 EEL = 146309.1322 RESTRAINT = 0.0000 ESURF = 986.7027 minimization completed, ENE= -.56627832E+05 RMS= 0.172297E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6751E+04 1.7234E+01 1.2765E+02 C 3729 BOND = 8283.5006 ANGLE = 22136.0974 DIHED = 32311.6040 VDWAALS = -24264.0449 EEL = -190606.2751 EGB = -62808.5741 1-4 VDW = 10745.4010 1-4 EEL = 146466.4182 RESTRAINT = 0.0000 ESURF = 984.9627 minimization completed, ENE= -.56750910E+05 RMS= 0.172344E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6452E+04 1.7287E+01 1.3759E+02 C 45875 BOND = 8434.3849 ANGLE = 22264.5198 DIHED = 32366.9056 VDWAALS = -24070.7105 EEL = -190398.9009 EGB = -62862.4452 1-4 VDW = 10719.8347 1-4 EEL = 146106.6186 RESTRAINT = 0.0000 ESURF = 987.3495 minimization completed, ENE= -.56452443E+05 RMS= 0.172868E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6519E+04 1.7400E+01 1.3952E+02 C 46933 BOND = 8411.5339 ANGLE = 22148.0893 DIHED = 32384.5409 VDWAALS = -24062.8191 EEL = -190372.0890 EGB = -63084.4583 1-4 VDW = 10772.5173 1-4 EEL = 146292.4004 RESTRAINT = 0.0000 ESURF = 991.3284 minimization completed, ENE= -.56518956E+05 RMS= 0.174004E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6662E+04 1.7329E+01 1.3715E+02 C 37822 BOND = 8378.7410 ANGLE = 22195.2162 DIHED = 32429.2620 VDWAALS = -24158.5457 EEL = -190505.5655 EGB = -62872.9023 1-4 VDW = 10650.3282 1-4 EEL = 146235.3821 RESTRAINT = 0.0000 ESURF = 986.2020 minimization completed, ENE= -.56661882E+05 RMS= 0.173292E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6508E+04 1.7279E+01 1.2851E+02 C 156 BOND = 8331.6481 ANGLE = 22164.8906 DIHED = 32307.7379 VDWAALS = -24117.3307 EEL = -190669.6114 EGB = -62643.5393 1-4 VDW = 10788.1087 1-4 EEL = 146338.2964 RESTRAINT = 0.0000 ESURF = 991.4896 minimization completed, ENE= -.56508310E+05 RMS= 0.172795E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6509E+04 1.7324E+01 1.2783E+02 CD 32493 BOND = 8373.1529 ANGLE = 22298.9627 DIHED = 32317.4985 VDWAALS = -24092.7255 EEL = -190561.1606 EGB = -62757.9126 1-4 VDW = 10769.1684 1-4 EEL = 146154.9831 RESTRAINT = 0.0000 ESURF = 989.0202 minimization completed, ENE= -.56509013E+05 RMS= 0.173239E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6182E+04 1.7435E+01 1.2949E+02 C 42904 BOND = 8453.0967 ANGLE = 22490.3271 DIHED = 32341.0019 VDWAALS = -24104.0945 EEL = -190902.3871 EGB = -62508.3919 1-4 VDW = 10784.6060 1-4 EEL = 146275.6704 RESTRAINT = 0.0000 ESURF = 988.0698 minimization completed, ENE= -.56182102E+05 RMS= 0.174347E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6466E+04 1.7355E+01 1.4130E+02 C 24624 BOND = 8388.5166 ANGLE = 22260.2646 DIHED = 32392.1844 VDWAALS = -24143.7021 EEL = -190246.3630 EGB = -62959.0985 1-4 VDW = 10752.6940 1-4 EEL = 146099.6236 RESTRAINT = 0.0000 ESURF = 989.8414 minimization completed, ENE= -.56466039E+05 RMS= 0.173546E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6548E+04 1.7359E+01 1.5537E+02 C 46009 BOND = 8417.7681 ANGLE = 22192.0020 DIHED = 32341.3612 VDWAALS = -24158.6429 EEL = -190834.2166 EGB = -62520.3660 1-4 VDW = 10790.3075 1-4 EEL = 146238.5426 RESTRAINT = 0.0000 ESURF = 985.2578 minimization completed, ENE= -.56547986E+05 RMS= 0.173587E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6445E+04 1.7421E+01 1.3697E+02 CA 27709 BOND = 8406.2052 ANGLE = 22214.6615 DIHED = 32323.8525 VDWAALS = -23919.4730 EEL = -191088.2627 EGB = -62503.7166 1-4 VDW = 10825.7756 1-4 EEL = 146302.3897 RESTRAINT = 0.0000 ESURF = 993.7105 minimization completed, ENE= -.56444857E+05 RMS= 0.174212E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6470E+04 1.7301E+01 1.1936E+02 CD 14732 BOND = 8341.5987 ANGLE = 22270.5465 DIHED = 32404.0779 VDWAALS = -24076.7274 EEL = -190766.5332 EGB = -62529.0747 1-4 VDW = 10666.2129 1-4 EEL = 146234.1811 RESTRAINT = 0.0000 ESURF = 986.1089 minimization completed, ENE= -.56469609E+05 RMS= 0.173006E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6641E+04 1.7259E+01 1.3874E+02 C 28939 BOND = 8376.7670 ANGLE = 22147.2255 DIHED = 32350.1396 VDWAALS = -24059.6749 EEL = -190266.6585 EGB = -62997.7832 1-4 VDW = 10769.7112 1-4 EEL = 146046.1551 RESTRAINT = 0.0000 ESURF = 992.9567 minimization completed, ENE= -.56641162E+05 RMS= 0.172592E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2837.94 ( 4.94% of Gen B) | Calc gb diag 13965.81 (24.30% of Gen B) | Calc gb off-diag 40677.10 (70.77% of Gen B) | Gen Born time 57480.87 (100.0% of Nonbo) | Nonbond force 57480.87 (100.0% of Force) | Bond/Angle/Dihedral 17.01 ( 0.03% of Force) | Force time 57498.21 (100.0% of Runmd) | Runmd Time 57498.21 (99.85% of Total) | Other 88.75 ( 0.15% of Total) | Total time 57587.20 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:31:51.020 on 10/17/2010 | Setup done at 07:31:53.887 on 10/17/2010 | Run done at 23:31:38.217 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:31:45 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.7 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.7 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6267E+04 1.7483E+01 1.3205E+02 CZ 44587 BOND = 8497.6652 ANGLE = 22335.8089 DIHED = 32431.9683 VDWAALS = -24047.3867 EEL = -190618.2884 EGB = -62703.5209 1-4 VDW = 10678.7781 1-4 EEL = 146163.8660 RESTRAINT = 0.0000 ESURF = 993.9229 minimization completed, ENE= -.56267187E+05 RMS= 0.174831E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6625E+04 1.7348E+01 1.2352E+02 C 7312 BOND = 8406.2697 ANGLE = 22057.5426 DIHED = 32338.6074 VDWAALS = -23951.5548 EEL = -190666.3346 EGB = -62849.9849 1-4 VDW = 10767.5882 1-4 EEL = 146275.2821 RESTRAINT = 0.0000 ESURF = 997.7176 minimization completed, ENE= -.56624867E+05 RMS= 0.173480E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6551E+04 1.7387E+01 1.3844E+02 CZ 2837 BOND = 8365.7161 ANGLE = 22295.0348 DIHED = 32359.0700 VDWAALS = -24013.7702 EEL = -190589.2816 EGB = -62911.6039 1-4 VDW = 10765.0444 1-4 EEL = 146185.3929 RESTRAINT = 0.0000 ESURF = 993.4467 minimization completed, ENE= -.56550951E+05 RMS= 0.173873E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6100E+04 1.7303E+01 1.2315E+02 C 27497 BOND = 8464.3993 ANGLE = 22545.4799 DIHED = 32398.1051 VDWAALS = -23881.1816 EEL = -190350.0921 EGB = -63071.5363 1-4 VDW = 10687.9412 1-4 EEL = 146112.1721 RESTRAINT = 0.0000 ESURF = 994.4276 minimization completed, ENE= -.56100285E+05 RMS= 0.173028E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6358E+04 1.7395E+01 1.5357E+02 CG 7978 BOND = 8431.3477 ANGLE = 22392.1612 DIHED = 32418.9873 VDWAALS = -23961.8264 EEL = -190643.5358 EGB = -62766.3392 1-4 VDW = 10699.7162 1-4 EEL = 146077.0834 RESTRAINT = 0.0000 ESURF = 994.5685 minimization completed, ENE= -.56357837E+05 RMS= 0.173952E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6418E+04 1.7256E+01 1.4166E+02 N 15743 BOND = 8300.0664 ANGLE = 22326.8704 DIHED = 32426.4671 VDWAALS = -24045.7280 EEL = -190419.4617 EGB = -62918.0856 1-4 VDW = 10713.5001 1-4 EEL = 146203.7174 RESTRAINT = 0.0000 ESURF = 994.9919 minimization completed, ENE= -.56417662E+05 RMS= 0.172561E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6704E+04 1.7302E+01 1.5272E+02 CG 7797 BOND = 8302.0013 ANGLE = 22312.2885 DIHED = 32256.1259 VDWAALS = -24063.8749 EEL = -190533.0969 EGB = -62872.1165 1-4 VDW = 10728.7015 1-4 EEL = 146177.5222 RESTRAINT = 0.0000 ESURF = 988.3449 minimization completed, ENE= -.56704104E+05 RMS= 0.173024E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6414E+04 1.7340E+01 1.3604E+02 C 26612 BOND = 8417.4548 ANGLE = 22319.0844 DIHED = 32502.9500 VDWAALS = -24012.7936 EEL = -190940.5462 EGB = -62508.7145 1-4 VDW = 10664.2164 1-4 EEL = 146155.8303 RESTRAINT = 0.0000 ESURF = 988.2082 minimization completed, ENE= -.56414310E+05 RMS= 0.173399E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6438E+04 1.7395E+01 1.1986E+02 C 11277 BOND = 8555.0353 ANGLE = 22326.1508 DIHED = 32405.8323 VDWAALS = -24083.4818 EEL = -190598.7657 EGB = -62790.5832 1-4 VDW = 10693.4086 1-4 EEL = 146062.5722 RESTRAINT = 0.0000 ESURF = 992.1154 minimization completed, ENE= -.56437716E+05 RMS= 0.173952E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6372E+04 1.7302E+01 1.2419E+02 CD 20417 BOND = 8373.5442 ANGLE = 22432.4122 DIHED = 32384.2177 VDWAALS = -24090.8212 EEL = -190650.6700 EGB = -62674.6219 1-4 VDW = 10730.6068 1-4 EEL = 146134.8332 RESTRAINT = 0.0000 ESURF = 988.9735 minimization completed, ENE= -.56371526E+05 RMS= 0.173017E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6755E+04 1.7387E+01 1.3361E+02 CD 31047 BOND = 8477.3440 ANGLE = 22150.5804 DIHED = 32310.3485 VDWAALS = -24028.5319 EEL = -190403.7182 EGB = -63116.3082 1-4 VDW = 10674.4968 1-4 EEL = 146190.3243 RESTRAINT = 0.0000 ESURF = 990.8339 minimization completed, ENE= -.56754631E+05 RMS= 0.173872E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6434E+04 1.7298E+01 1.4504E+02 C 41816 BOND = 8347.4854 ANGLE = 22347.5623 DIHED = 32336.7690 VDWAALS = -23939.3441 EEL = -190627.0250 EGB = -62702.3821 1-4 VDW = 10736.0022 1-4 EEL = 146081.4026 RESTRAINT = 0.0000 ESURF = 985.6648 minimization completed, ENE= -.56433865E+05 RMS= 0.172980E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6544E+04 1.7377E+01 1.2705E+02 CG 7887 BOND = 8526.5483 ANGLE = 22324.6538 DIHED = 32341.5933 VDWAALS = -24104.4121 EEL = -190396.7603 EGB = -63128.1006 1-4 VDW = 10648.1656 1-4 EEL = 146249.5860 RESTRAINT = 0.0000 ESURF = 994.4922 minimization completed, ENE= -.56544234E+05 RMS= 0.173766E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6723E+04 1.7280E+01 1.2848E+02 C 10761 BOND = 8371.8286 ANGLE = 22172.1501 DIHED = 32318.2639 VDWAALS = -24016.8901 EEL = -190947.5854 EGB = -62653.0677 1-4 VDW = 10742.8104 1-4 EEL = 146299.1732 RESTRAINT = 0.0000 ESURF = 990.3413 minimization completed, ENE= -.56722976E+05 RMS= 0.172800E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6484E+04 1.7299E+01 1.2035E+02 C 2767 BOND = 8480.6653 ANGLE = 22255.8215 DIHED = 32432.4327 VDWAALS = -24094.9289 EEL = -190632.7725 EGB = -62752.2734 1-4 VDW = 10695.2617 1-4 EEL = 146144.4398 RESTRAINT = 0.0000 ESURF = 987.4479 minimization completed, ENE= -.56483906E+05 RMS= 0.172989E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6743E+04 1.7377E+01 1.4000E+02 CD 1499 BOND = 8463.3831 ANGLE = 22155.4237 DIHED = 32222.7123 VDWAALS = -23972.4679 EEL = -190401.9981 EGB = -63125.3529 1-4 VDW = 10764.2389 1-4 EEL = 146156.5217 RESTRAINT = 0.0000 ESURF = 994.4819 minimization completed, ENE= -.56743057E+05 RMS= 0.173770E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6429E+04 1.7385E+01 1.5145E+02 C 11707 BOND = 8385.6547 ANGLE = 22168.6998 DIHED = 32318.7724 VDWAALS = -24053.7821 EEL = -190426.3357 EGB = -62891.9928 1-4 VDW = 10803.4265 1-4 EEL = 146275.3007 RESTRAINT = 0.0000 ESURF = 991.4321 minimization completed, ENE= -.56428824E+05 RMS= 0.173854E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6712E+04 1.7273E+01 1.4097E+02 C 29782 BOND = 8340.6520 ANGLE = 22166.7751 DIHED = 32358.1949 VDWAALS = -24138.4712 EEL = -190161.0327 EGB = -63311.0253 1-4 VDW = 10733.0940 1-4 EEL = 146307.6132 RESTRAINT = 0.0000 ESURF = 992.6447 minimization completed, ENE= -.56711555E+05 RMS= 0.172726E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6448E+04 1.7343E+01 1.2904E+02 N 14095 BOND = 8439.1961 ANGLE = 22145.0522 DIHED = 32278.9712 VDWAALS = -24117.5813 EEL = -190036.5568 EGB = -63173.0587 1-4 VDW = 10737.4121 1-4 EEL = 146287.9660 RESTRAINT = 0.0000 ESURF = 990.7902 minimization completed, ENE= -.56447809E+05 RMS= 0.173431E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6471E+04 1.7309E+01 1.3199E+02 C 31575 BOND = 8443.8516 ANGLE = 22108.8780 DIHED = 32411.5812 VDWAALS = -23993.9625 EEL = -189965.1318 EGB = -63317.1317 1-4 VDW = 10685.1498 1-4 EEL = 146162.1739 RESTRAINT = 0.0000 ESURF = 993.9829 minimization completed, ENE= -.56470609E+05 RMS= 0.173087E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6679E+04 1.7324E+01 1.1728E+02 C 10911 BOND = 8364.7917 ANGLE = 22278.7217 DIHED = 32301.7077 VDWAALS = -23965.8138 EEL = -190605.1762 EGB = -62906.9727 1-4 VDW = 10729.2513 1-4 EEL = 146132.5096 RESTRAINT = 0.0000 ESURF = 992.2322 minimization completed, ENE= -.56678749E+05 RMS= 0.173238E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6648E+04 1.7354E+01 1.4375E+02 CD 39067 BOND = 8481.8365 ANGLE = 22227.0483 DIHED = 32293.1952 VDWAALS = -24056.4515 EEL = -190967.5223 EGB = -62677.0630 1-4 VDW = 10770.9638 1-4 EEL = 146287.4854 RESTRAINT = 0.0000 ESURF = 992.4824 minimization completed, ENE= -.56648025E+05 RMS= 0.173538E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6464E+04 1.7353E+01 1.3226E+02 C 33861 BOND = 8551.7411 ANGLE = 22203.1029 DIHED = 32417.6427 VDWAALS = -24139.0908 EEL = -190270.3625 EGB = -62902.4064 1-4 VDW = 10664.1378 1-4 EEL = 146020.5243 RESTRAINT = 0.0000 ESURF = 990.5861 minimization completed, ENE= -.56464125E+05 RMS= 0.173532E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6559E+04 1.7364E+01 1.3414E+02 CD 22567 BOND = 8369.5570 ANGLE = 22304.4628 DIHED = 32357.8831 VDWAALS = -23996.3933 EEL = -190312.3735 EGB = -63266.6492 1-4 VDW = 10709.5200 1-4 EEL = 146275.8027 RESTRAINT = 0.0000 ESURF = 998.8712 minimization completed, ENE= -.56559319E+05 RMS= 0.173637E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6544E+04 1.7373E+01 1.4531E+02 C 12742 BOND = 8438.4052 ANGLE = 22246.6174 DIHED = 32259.3392 VDWAALS = -24065.8521 EEL = -190107.3759 EGB = -63250.2498 1-4 VDW = 10672.1715 1-4 EEL = 146269.5344 RESTRAINT = 0.0000 ESURF = 993.3649 minimization completed, ENE= -.56544045E+05 RMS= 0.173729E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2828.19 ( 4.94% of Gen B) | Calc gb diag 13978.94 (24.43% of Gen B) | Calc gb off-diag 40415.71 (70.63% of Gen B) | Gen Born time 57223.15 (100.0% of Nonbo) | Nonbond force 57223.15 (100.0% of Force) | Bond/Angle/Dihedral 15.66 ( 0.03% of Force) | Force time 57238.85 (100.0% of Runmd) | Runmd Time 57238.85 (99.85% of Total) | Other 87.39 ( 0.15% of Total) | Total time 57326.36 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:31:45.146 on 10/17/2010 | Setup done at 07:31:48.125 on 10/17/2010 | Run done at 23:27:11.510 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:31:39 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.6 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.6 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6509E+04 1.7427E+01 1.4698E+02 CG 20012 BOND = 8464.8670 ANGLE = 22113.2875 DIHED = 32422.8708 VDWAALS = -23939.1345 EEL = -190764.1487 EGB = -62829.5075 1-4 VDW = 10752.2028 1-4 EEL = 146276.5847 RESTRAINT = 0.0000 ESURF = 993.6419 minimization completed, ENE= -.56509336E+05 RMS= 0.174275E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6755E+04 1.7398E+01 1.4795E+02 N 1061 BOND = 8430.9529 ANGLE = 22044.7963 DIHED = 32357.3756 VDWAALS = -23978.8709 EEL = -190592.0559 EGB = -63026.6169 1-4 VDW = 10705.0079 1-4 EEL = 146311.6952 RESTRAINT = 0.0000 ESURF = 993.0571 minimization completed, ENE= -.56754659E+05 RMS= 0.173978E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6355E+04 1.7329E+01 1.3036E+02 CD1 2896 BOND = 8383.3579 ANGLE = 22435.1207 DIHED = 32356.7002 VDWAALS = -24063.0095 EEL = -190183.3020 EGB = -63312.2205 1-4 VDW = 10720.8783 1-4 EEL = 146312.4957 RESTRAINT = 0.0000 ESURF = 995.4292 minimization completed, ENE= -.56354550E+05 RMS= 0.173288E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6380E+04 1.7317E+01 1.3753E+02 C 21418 BOND = 8446.6346 ANGLE = 22291.8266 DIHED = 32315.4303 VDWAALS = -24002.3320 EEL = -189978.7288 EGB = -63262.2491 1-4 VDW = 10765.0175 1-4 EEL = 146051.0558 RESTRAINT = 0.0000 ESURF = 993.5568 minimization completed, ENE= -.56379788E+05 RMS= 0.173172E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6483E+04 1.7332E+01 1.4128E+02 CG 2429 BOND = 8453.2301 ANGLE = 22315.0140 DIHED = 32382.0741 VDWAALS = -24117.9458 EEL = -190132.7189 EGB = -63242.4687 1-4 VDW = 10714.6277 1-4 EEL = 146151.4307 RESTRAINT = 0.0000 ESURF = 993.2631 minimization completed, ENE= -.56483494E+05 RMS= 0.173316E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6513E+04 1.7426E+01 1.3290E+02 C 1812 BOND = 8482.1761 ANGLE = 22233.5421 DIHED = 32472.8466 VDWAALS = -24104.8539 EEL = -190673.7371 EGB = -62962.1658 1-4 VDW = 10735.1658 1-4 EEL = 146311.3803 RESTRAINT = 0.0000 ESURF = 992.3339 minimization completed, ENE= -.56513312E+05 RMS= 0.174256E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6203E+04 1.7512E+01 1.1936E+02 C 25806 BOND = 8581.2281 ANGLE = 22353.1176 DIHED = 32473.6561 VDWAALS = -23864.3597 EEL = -190888.1175 EGB = -62704.7661 1-4 VDW = 10717.6141 1-4 EEL = 146127.8849 RESTRAINT = 0.0000 ESURF = 1000.3453 minimization completed, ENE= -.56203397E+05 RMS= 0.175117E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6367E+04 1.7374E+01 1.3185E+02 C 40600 BOND = 8439.8310 ANGLE = 22245.4035 DIHED = 32461.9910 VDWAALS = -24073.6829 EEL = -190506.6543 EGB = -63098.0150 1-4 VDW = 10773.5093 1-4 EEL = 146400.2003 RESTRAINT = 0.0000 ESURF = 990.5307 minimization completed, ENE= -.56366886E+05 RMS= 0.173737E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6520E+04 1.7378E+01 1.3478E+02 CG 6491 BOND = 8372.8339 ANGLE = 22189.1721 DIHED = 32407.0080 VDWAALS = -24049.1215 EEL = -190102.0465 EGB = -63261.6682 1-4 VDW = 10709.8302 1-4 EEL = 146222.9705 RESTRAINT = 0.0000 ESURF = 990.8754 minimization completed, ENE= -.56520146E+05 RMS= 0.173777E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6623E+04 1.7248E+01 1.2466E+02 CG 7090 BOND = 8288.0197 ANGLE = 22304.7816 DIHED = 32426.1168 VDWAALS = -24153.5555 EEL = -190659.4178 EGB = -62842.9836 1-4 VDW = 10691.9491 1-4 EEL = 146329.2967 RESTRAINT = 0.0000 ESURF = 993.1702 minimization completed, ENE= -.56622623E+05 RMS= 0.172476E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6628E+04 1.7411E+01 1.2097E+02 C 9500 BOND = 8483.3121 ANGLE = 22240.2915 DIHED = 32378.6157 VDWAALS = -23941.5608 EEL = -190649.9797 EGB = -62908.9319 1-4 VDW = 10676.7132 1-4 EEL = 146098.5184 RESTRAINT = 0.0000 ESURF = 995.2243 minimization completed, ENE= -.56627797E+05 RMS= 0.174106E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6465E+04 1.7413E+01 1.3185E+02 C 6878 BOND = 8536.5431 ANGLE = 22229.4603 DIHED = 32352.7514 VDWAALS = -23970.0471 EEL = -190704.0761 EGB = -62748.2175 1-4 VDW = 10734.2810 1-4 EEL = 146112.7023 RESTRAINT = 0.0000 ESURF = 991.1146 minimization completed, ENE= -.56465488E+05 RMS= 0.174131E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6812E+04 1.7250E+01 1.2992E+02 CG 36244 BOND = 8378.4636 ANGLE = 22059.3880 DIHED = 32380.8665 VDWAALS = -24059.8206 EEL = -190986.1102 EGB = -62762.3306 1-4 VDW = 10710.0158 1-4 EEL = 146467.3836 RESTRAINT = 0.0000 ESURF = 1000.4279 minimization completed, ENE= -.56811716E+05 RMS= 0.172503E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6561E+04 1.7383E+01 1.2526E+02 C 19986 BOND = 8419.0641 ANGLE = 22178.0935 DIHED = 32368.7663 VDWAALS = -23993.8510 EEL = -190824.6471 EGB = -62825.5591 1-4 VDW = 10769.8365 1-4 EEL = 146350.6555 RESTRAINT = 0.0000 ESURF = 996.7591 minimization completed, ENE= -.56560882E+05 RMS= 0.173828E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6685E+04 1.7401E+01 1.3696E+02 CZ 16206 BOND = 8473.1405 ANGLE = 22120.6367 DIHED = 32381.8540 VDWAALS = -23940.0982 EEL = -191258.9545 EGB = -62453.9135 1-4 VDW = 10779.0380 1-4 EEL = 146216.4508 RESTRAINT = 0.0000 ESURF = 996.9250 minimization completed, ENE= -.56684921E+05 RMS= 0.174008E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6356E+04 1.7361E+01 1.1330E+02 C 30515 BOND = 8529.5979 ANGLE = 22421.3344 DIHED = 32312.7355 VDWAALS = -24061.8314 EEL = -190574.4871 EGB = -62828.7827 1-4 VDW = 10739.2049 1-4 EEL = 146110.7980 RESTRAINT = 0.0000 ESURF = 995.9094 minimization completed, ENE= -.56355521E+05 RMS= 0.173605E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6179E+04 1.7453E+01 1.1665E+02 CD 22191 BOND = 8476.4509 ANGLE = 22410.5801 DIHED = 32424.3735 VDWAALS = -24005.5525 EEL = -190403.8821 EGB = -62985.5173 1-4 VDW = 10731.9447 1-4 EEL = 146177.9175 RESTRAINT = 0.0000 ESURF = 994.3635 minimization completed, ENE= -.56179322E+05 RMS= 0.174526E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6454E+04 1.7317E+01 1.2398E+02 C 40331 BOND = 8321.6169 ANGLE = 22429.2148 DIHED = 32399.7288 VDWAALS = -24073.6798 EEL = -190308.8632 EGB = -63272.2161 1-4 VDW = 10706.2334 1-4 EEL = 146350.1852 RESTRAINT = 0.0000 ESURF = 993.7740 minimization completed, ENE= -.56454006E+05 RMS= 0.173169E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6586E+04 1.7222E+01 1.2471E+02 C 17879 BOND = 8390.6999 ANGLE = 22221.1602 DIHED = 32465.7757 VDWAALS = -24074.5056 EEL = -190213.1949 EGB = -63293.7689 1-4 VDW = 10690.0551 1-4 EEL = 146231.4997 RESTRAINT = 0.0000 ESURF = 995.9633 minimization completed, ENE= -.56586316E+05 RMS= 0.172217E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6434E+04 1.7397E+01 1.3714E+02 N 4970 BOND = 8454.6687 ANGLE = 22261.3095 DIHED = 32335.1723 VDWAALS = -23914.1163 EEL = -190569.8265 EGB = -62992.5094 1-4 VDW = 10774.2842 1-4 EEL = 146220.9302 RESTRAINT = 0.0000 ESURF = 995.8723 minimization completed, ENE= -.56434215E+05 RMS= 0.173970E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6692E+04 1.7323E+01 1.2636E+02 C 23295 BOND = 8303.3651 ANGLE = 22175.6771 DIHED = 32392.6925 VDWAALS = -24015.3062 EEL = -190806.0124 EGB = -62982.8189 1-4 VDW = 10770.7944 1-4 EEL = 146469.8620 RESTRAINT = 0.0000 ESURF = 999.5464 minimization completed, ENE= -.56692200E+05 RMS= 0.173226E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6423E+04 1.7260E+01 1.4493E+02 C 3710 BOND = 8323.2417 ANGLE = 22291.4591 DIHED = 32398.6338 VDWAALS = -23906.0751 EEL = -190879.1503 EGB = -62699.6212 1-4 VDW = 10767.1821 1-4 EEL = 146293.5592 RESTRAINT = 0.0000 ESURF = 987.6715 minimization completed, ENE= -.56423099E+05 RMS= 0.172599E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6651E+04 1.7443E+01 1.2149E+02 N 9579 BOND = 8488.3240 ANGLE = 22152.6038 DIHED = 32384.2124 VDWAALS = -24091.0684 EEL = -190564.7699 EGB = -62959.3827 1-4 VDW = 10736.1717 1-4 EEL = 146213.5295 RESTRAINT = 0.0000 ESURF = 989.2907 minimization completed, ENE= -.56651089E+05 RMS= 0.174435E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6657E+04 1.7217E+01 1.2656E+02 C 22395 BOND = 8451.5802 ANGLE = 22087.5748 DIHED = 32275.9237 VDWAALS = -24006.3763 EEL = -190307.4601 EGB = -63021.0309 1-4 VDW = 10767.1342 1-4 EEL = 146102.4626 RESTRAINT = 0.0000 ESURF = 993.0023 minimization completed, ENE= -.56657190E+05 RMS= 0.172169E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6803E+04 1.7187E+01 1.5463E+02 CD 13609 BOND = 8284.6422 ANGLE = 22241.3705 DIHED = 32437.2173 VDWAALS = -23955.8349 EEL = -191231.7015 EGB = -62553.3566 1-4 VDW = 10740.4589 1-4 EEL = 146244.6050 RESTRAINT = 0.0000 ESURF = 989.5256 minimization completed, ENE= -.56803073E+05 RMS= 0.171866E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2845.13 ( 4.95% of Gen B) | Calc gb diag 13950.49 (24.29% of Gen B) | Calc gb off-diag 40641.19 (70.76% of Gen B) | Gen Born time 57436.82 (100.0% of Nonbo) | Nonbond force 57436.82 (100.0% of Force) | Bond/Angle/Dihedral 16.27 ( 0.03% of Force) | Force time 57453.42 (100.0% of Runmd) | Runmd Time 57453.42 (99.84% of Total) | Other 93.35 ( 0.16% of Total) | Total time 57546.89 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:31:39.441 on 10/17/2010 | Setup done at 07:31:43.395 on 10/17/2010 | Run done at 23:30:46.329 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:31:33 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.5 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.5 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6506E+04 1.7403E+01 1.1943E+02 CZ 24041 BOND = 8432.4809 ANGLE = 22272.6645 DIHED = 32405.3825 VDWAALS = -24064.7350 EEL = -190542.6937 EGB = -62873.4876 1-4 VDW = 10703.5491 1-4 EEL = 146164.8721 RESTRAINT = 0.0000 ESURF = 995.9875 minimization completed, ENE= -.56505980E+05 RMS= 0.174026E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6504E+04 1.7312E+01 1.5380E+02 CD 39067 BOND = 8398.4569 ANGLE = 22291.0998 DIHED = 32472.1147 VDWAALS = -24072.7946 EEL = -190794.0062 EGB = -62726.9168 1-4 VDW = 10747.7294 1-4 EEL = 146184.8956 RESTRAINT = 0.0000 ESURF = 995.4752 minimization completed, ENE= -.56503946E+05 RMS= 0.173120E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6450E+04 1.7342E+01 1.2438E+02 N 19042 BOND = 8361.6427 ANGLE = 22394.3814 DIHED = 32457.5610 VDWAALS = -24051.8985 EEL = -190681.7485 EGB = -62819.2485 1-4 VDW = 10741.7291 1-4 EEL = 146158.0804 RESTRAINT = 0.0000 ESURF = 989.8659 minimization completed, ENE= -.56449635E+05 RMS= 0.173419E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6667E+04 1.7263E+01 1.3192E+02 C 33538 BOND = 8403.6458 ANGLE = 22127.3447 DIHED = 32453.6399 VDWAALS = -24193.0250 EEL = -190462.0275 EGB = -62792.1707 1-4 VDW = 10650.1597 1-4 EEL = 146154.0804 RESTRAINT = 0.0000 ESURF = 990.9484 minimization completed, ENE= -.56667404E+05 RMS= 0.172631E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6469E+04 1.7375E+01 1.2690E+02 C 31948 BOND = 8341.8104 ANGLE = 22351.4923 DIHED = 32369.1241 VDWAALS = -24096.1573 EEL = -190092.2389 EGB = -63212.5658 1-4 VDW = 10791.6121 1-4 EEL = 146084.6613 RESTRAINT = 0.0000 ESURF = 992.9076 minimization completed, ENE= -.56469354E+05 RMS= 0.173751E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6707E+04 1.7276E+01 1.4519E+02 CD 26944 BOND = 8377.5521 ANGLE = 21985.7516 DIHED = 32459.1356 VDWAALS = -24046.5933 EEL = -190531.0425 EGB = -63199.3450 1-4 VDW = 10791.3203 1-4 EEL = 146458.7718 RESTRAINT = 0.0000 ESURF = 997.8999 minimization completed, ENE= -.56706550E+05 RMS= 0.172760E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6579E+04 1.7359E+01 1.2268E+02 C 23925 BOND = 8323.1346 ANGLE = 22161.4987 DIHED = 32355.2016 VDWAALS = -24086.9116 EEL = -190818.6684 EGB = -62718.6257 1-4 VDW = 10814.3800 1-4 EEL = 146393.1853 RESTRAINT = 0.0000 ESURF = 998.1327 minimization completed, ENE= -.56578673E+05 RMS= 0.173591E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6773E+04 1.7293E+01 1.2279E+02 N 20607 BOND = 8404.5979 ANGLE = 22007.6903 DIHED = 32353.0229 VDWAALS = -24103.0016 EEL = -190812.2082 EGB = -62599.1821 1-4 VDW = 10794.3908 1-4 EEL = 146187.3439 RESTRAINT = 0.0000 ESURF = 994.0370 minimization completed, ENE= -.56773309E+05 RMS= 0.172928E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6715E+04 1.7247E+01 1.3060E+02 C 6683 BOND = 8384.7516 ANGLE = 22310.7593 DIHED = 32351.3010 VDWAALS = -24033.1370 EEL = -190400.9889 EGB = -63152.0468 1-4 VDW = 10698.4249 1-4 EEL = 146126.1536 RESTRAINT = 0.0000 ESURF = 999.9376 minimization completed, ENE= -.56714845E+05 RMS= 0.172469E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6579E+04 1.7264E+01 1.4951E+02 N 22490 BOND = 8299.9283 ANGLE = 22229.6559 DIHED = 32447.6217 VDWAALS = -24090.3486 EEL = -190155.7312 EGB = -63333.7368 1-4 VDW = 10737.1091 1-4 EEL = 146284.7714 RESTRAINT = 0.0000 ESURF = 1001.8018 minimization completed, ENE= -.56578928E+05 RMS= 0.172641E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6818E+04 1.7260E+01 1.1976E+02 C 17629 BOND = 8390.2594 ANGLE = 22129.9079 DIHED = 32351.3373 VDWAALS = -23982.8544 EEL = -190697.9830 EGB = -63060.4880 1-4 VDW = 10732.0723 1-4 EEL = 146318.6137 RESTRAINT = 0.0000 ESURF = 1000.7377 minimization completed, ENE= -.56818397E+05 RMS= 0.172597E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6470E+04 1.7430E+01 1.3582E+02 C 46009 BOND = 8463.0309 ANGLE = 22285.7222 DIHED = 32373.3032 VDWAALS = -24012.2476 EEL = -190458.1151 EGB = -63310.5073 1-4 VDW = 10773.1869 1-4 EEL = 146417.9365 RESTRAINT = 0.0000 ESURF = 997.8298 minimization completed, ENE= -.56469861E+05 RMS= 0.174304E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6393E+04 1.7372E+01 1.2397E+02 C 20832 BOND = 8378.1831 ANGLE = 22364.9266 DIHED = 32340.5174 VDWAALS = -24038.7947 EEL = -190267.2047 EGB = -63238.2346 1-4 VDW = 10796.3954 1-4 EEL = 146276.0002 RESTRAINT = 0.0000 ESURF = 995.5583 minimization completed, ENE= -.56392653E+05 RMS= 0.173725E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6542E+04 1.7365E+01 1.2644E+02 C 38218 BOND = 8491.2907 ANGLE = 22376.7391 DIHED = 32300.1919 VDWAALS = -24118.8356 EEL = -190447.9722 EGB = -63027.9954 1-4 VDW = 10646.2218 1-4 EEL = 146238.1128 RESTRAINT = 0.0000 ESURF = 999.8594 minimization completed, ENE= -.56542387E+05 RMS= 0.173653E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6510E+04 1.7366E+01 1.5045E+02 C 45414 BOND = 8377.0972 ANGLE = 22433.7153 DIHED = 32484.3308 VDWAALS = -23933.8476 EEL = -190918.1680 EGB = -63126.7745 1-4 VDW = 10758.3511 1-4 EEL = 146415.2737 RESTRAINT = 0.0000 ESURF = 1000.1221 minimization completed, ENE= -.56509900E+05 RMS= 0.173659E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6617E+04 1.7305E+01 1.3332E+02 C 32974 BOND = 8369.4342 ANGLE = 22321.5929 DIHED = 32405.6018 VDWAALS = -23999.7987 EEL = -190877.7767 EGB = -62870.3143 1-4 VDW = 10787.9554 1-4 EEL = 146253.1702 RESTRAINT = 0.0000 ESURF = 993.0446 minimization completed, ENE= -.56617090E+05 RMS= 0.173050E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6801E+04 1.7261E+01 1.3113E+02 C 31073 BOND = 8364.1752 ANGLE = 22119.9476 DIHED = 32347.7900 VDWAALS = -24055.1137 EEL = -190493.5785 EGB = -63024.7000 1-4 VDW = 10705.6550 1-4 EEL = 146239.4826 RESTRAINT = 0.0000 ESURF = 995.1786 minimization completed, ENE= -.56801163E+05 RMS= 0.172612E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6358E+04 1.7470E+01 1.2844E+02 CG 22176 BOND = 8382.3536 ANGLE = 22494.6241 DIHED = 32394.5490 VDWAALS = -24044.7148 EEL = -190847.1198 EGB = -62778.5381 1-4 VDW = 10827.4783 1-4 EEL = 146223.6688 RESTRAINT = 0.0000 ESURF = 989.4433 minimization completed, ENE= -.56358256E+05 RMS= 0.174704E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6470E+04 1.7450E+01 1.2966E+02 C 17019 BOND = 8420.9491 ANGLE = 22251.7128 DIHED = 32341.8584 VDWAALS = -23979.1231 EEL = -190674.1912 EGB = -62969.4077 1-4 VDW = 10780.7859 1-4 EEL = 146365.1409 RESTRAINT = 0.0000 ESURF = 992.1421 minimization completed, ENE= -.56470133E+05 RMS= 0.174501E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6598E+04 1.7265E+01 1.3415E+02 C 1182 BOND = 8243.5879 ANGLE = 22412.8915 DIHED = 32333.9888 VDWAALS = -24090.7526 EEL = -190364.4130 EGB = -63068.8360 1-4 VDW = 10717.0833 1-4 EEL = 146227.7859 RESTRAINT = 0.0000 ESURF = 990.4052 minimization completed, ENE= -.56598259E+05 RMS= 0.172646E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6798E+04 1.7281E+01 1.4470E+02 C 41816 BOND = 8364.3099 ANGLE = 22257.3081 DIHED = 32339.9359 VDWAALS = -24150.6807 EEL = -190242.3694 EGB = -63303.5349 1-4 VDW = 10726.6375 1-4 EEL = 146218.8059 RESTRAINT = 0.0000 ESURF = 991.7787 minimization completed, ENE= -.56797809E+05 RMS= 0.172814E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6517E+04 1.7375E+01 1.2121E+02 C 9322 BOND = 8433.1898 ANGLE = 22385.4502 DIHED = 32363.0236 VDWAALS = -24148.5228 EEL = -190555.2063 EGB = -63050.5917 1-4 VDW = 10612.2200 1-4 EEL = 146449.3460 RESTRAINT = 0.0000 ESURF = 993.6068 minimization completed, ENE= -.56517484E+05 RMS= 0.173755E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6542E+04 1.7307E+01 1.3444E+02 CZ 37777 BOND = 8510.9908 ANGLE = 22116.1731 DIHED = 32344.8735 VDWAALS = -24140.8100 EEL = -190552.3707 EGB = -63013.1018 1-4 VDW = 10729.3317 1-4 EEL = 146470.2935 RESTRAINT = 0.0000 ESURF = 992.6896 minimization completed, ENE= -.56541930E+05 RMS= 0.173067E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6512E+04 1.7345E+01 1.3317E+02 CD1 36712 BOND = 8452.6705 ANGLE = 22201.0175 DIHED = 32357.0220 VDWAALS = -24052.4133 EEL = -190524.7427 EGB = -63095.3302 1-4 VDW = 10804.9700 1-4 EEL = 146347.6064 RESTRAINT = 0.0000 ESURF = 997.2554 minimization completed, ENE= -.56511944E+05 RMS= 0.173448E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6558E+04 1.7275E+01 1.3515E+02 CA 14554 BOND = 8390.8466 ANGLE = 22301.4040 DIHED = 32361.4289 VDWAALS = -24105.9153 EEL = -190697.1142 EGB = -62822.7252 1-4 VDW = 10672.6015 1-4 EEL = 146345.0036 RESTRAINT = 0.0000 ESURF = 996.4372 minimization completed, ENE= -.56558033E+05 RMS= 0.172746E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2835.76 ( 4.95% of Gen B) | Calc gb diag 13971.16 (24.39% of Gen B) | Calc gb off-diag 40484.96 (70.66% of Gen B) | Gen Born time 57291.89 (100.0% of Nonbo) | Nonbond force 57291.89 (100.0% of Force) | Bond/Angle/Dihedral 17.49 ( 0.03% of Force) | Force time 57309.41 (100.0% of Runmd) | Runmd Time 57309.41 (99.83% of Total) | Other 96.31 ( 0.17% of Total) | Total time 57405.88 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:31:33.091 on 10/17/2010 | Setup done at 07:31:36.656 on 10/17/2010 | Run done at 23:28:18.968 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:31:27 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.4 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.4 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6659E+04 1.7392E+01 1.4315E+02 CG 40462 BOND = 8391.7224 ANGLE = 22166.4118 DIHED = 32415.8566 VDWAALS = -24106.8029 EEL = -190427.8974 EGB = -63206.4460 1-4 VDW = 10723.2607 1-4 EEL = 146389.6714 RESTRAINT = 0.0000 ESURF = 995.4659 minimization completed, ENE= -.56658758E+05 RMS= 0.173922E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6504E+04 1.7332E+01 1.2253E+02 C 24816 BOND = 8370.0691 ANGLE = 22197.7656 DIHED = 32393.8530 VDWAALS = -24066.4786 EEL = -190566.1584 EGB = -62956.5994 1-4 VDW = 10811.3864 1-4 EEL = 146318.5886 RESTRAINT = 0.0000 ESURF = 993.3630 minimization completed, ENE= -.56504211E+05 RMS= 0.173317E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6704E+04 1.7342E+01 1.4900E+02 NE 12074 BOND = 8474.4269 ANGLE = 22055.7966 DIHED = 32358.3748 VDWAALS = -24095.6446 EEL = -190514.9182 EGB = -63059.8848 1-4 VDW = 10739.3588 1-4 EEL = 146347.0008 RESTRAINT = 0.0000 ESURF = 991.8504 minimization completed, ENE= -.56703639E+05 RMS= 0.173418E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6623E+04 1.7341E+01 1.2538E+02 CD 41773 BOND = 8473.8543 ANGLE = 22333.2729 DIHED = 32381.1365 VDWAALS = -24124.9033 EEL = -190798.8330 EGB = -62728.2408 1-4 VDW = 10726.5619 1-4 EEL = 146120.1130 RESTRAINT = 0.0000 ESURF = 994.2328 minimization completed, ENE= -.56622806E+05 RMS= 0.173408E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6252E+04 1.7334E+01 1.3878E+02 C 9977 BOND = 8436.2952 ANGLE = 22406.6072 DIHED = 32542.1195 VDWAALS = -24092.3857 EEL = -191022.9286 EGB = -62505.1861 1-4 VDW = 10718.4506 1-4 EEL = 146274.4214 RESTRAINT = 0.0000 ESURF = 990.1381 minimization completed, ENE= -.56252468E+05 RMS= 0.173338E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6556E+04 1.7412E+01 1.2891E+02 C 2751 BOND = 8431.0658 ANGLE = 22189.0839 DIHED = 32353.0173 VDWAALS = -24075.4824 EEL = -190888.4642 EGB = -62760.3729 1-4 VDW = 10735.3656 1-4 EEL = 146466.2837 RESTRAINT = 0.0000 ESURF = 993.4215 minimization completed, ENE= -.56556082E+05 RMS= 0.174122E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6346E+04 1.7370E+01 1.2314E+02 C 4551 BOND = 8376.4401 ANGLE = 22570.4520 DIHED = 32381.2363 VDWAALS = -24129.3680 EEL = -191001.4419 EGB = -62495.3484 1-4 VDW = 10731.2248 1-4 EEL = 146225.4220 RESTRAINT = 0.0000 ESURF = 995.5634 minimization completed, ENE= -.56345820E+05 RMS= 0.173704E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6610E+04 1.7284E+01 1.2323E+02 C 25398 BOND = 8399.1787 ANGLE = 22199.5516 DIHED = 32488.8387 VDWAALS = -24131.5863 EEL = -190953.3185 EGB = -62684.8449 1-4 VDW = 10779.2807 1-4 EEL = 146295.6617 RESTRAINT = 0.0000 ESURF = 997.6612 minimization completed, ENE= -.56609577E+05 RMS= 0.172840E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6951E+04 1.7242E+01 1.3213E+02 CA 6653 BOND = 8320.0788 ANGLE = 22106.2282 DIHED = 32377.1805 VDWAALS = -24032.2939 EEL = -191321.9800 EGB = -62411.2890 1-4 VDW = 10739.4475 1-4 EEL = 146279.3633 RESTRAINT = 0.0000 ESURF = 992.1278 minimization completed, ENE= -.56951137E+05 RMS= 0.172422E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6597E+04 1.7368E+01 1.2815E+02 C 18226 BOND = 8417.4954 ANGLE = 22433.8832 DIHED = 32380.8256 VDWAALS = -24082.2873 EEL = -191034.4834 EGB = -62698.7236 1-4 VDW = 10729.8847 1-4 EEL = 146265.6093 RESTRAINT = 0.0000 ESURF = 991.1421 minimization completed, ENE= -.56596654E+05 RMS= 0.173677E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6446E+04 1.7336E+01 1.2695E+02 CD 23212 BOND = 8352.4575 ANGLE = 22320.2353 DIHED = 32396.5111 VDWAALS = -24081.8929 EEL = -191134.1990 EGB = -62449.9759 1-4 VDW = 10833.1709 1-4 EEL = 146327.3013 RESTRAINT = 0.0000 ESURF = 990.5092 minimization completed, ENE= -.56445882E+05 RMS= 0.173361E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6497E+04 1.7305E+01 1.2527E+02 N 559 BOND = 8462.4766 ANGLE = 22374.4121 DIHED = 32415.0450 VDWAALS = -24014.5399 EEL = -190900.8239 EGB = -62651.5449 1-4 VDW = 10645.7729 1-4 EEL = 146179.6515 RESTRAINT = 0.0000 ESURF = 992.3709 minimization completed, ENE= -.56497180E+05 RMS= 0.173052E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6560E+04 1.7406E+01 1.2335E+02 C 37393 BOND = 8455.3181 ANGLE = 22294.0764 DIHED = 32395.7125 VDWAALS = -23982.0645 EEL = -191248.5299 EGB = -62533.0387 1-4 VDW = 10732.7107 1-4 EEL = 146334.4763 RESTRAINT = 0.0000 ESURF = 991.5794 minimization completed, ENE= -.56559760E+05 RMS= 0.174063E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6768E+04 1.7260E+01 1.2528E+02 C 14916 BOND = 8277.2627 ANGLE = 22197.2651 DIHED = 32393.8423 VDWAALS = -24066.8862 EEL = -190896.4816 EGB = -62669.1714 1-4 VDW = 10739.3303 1-4 EEL = 146259.6859 RESTRAINT = 0.0000 ESURF = 997.2590 minimization completed, ENE= -.56767894E+05 RMS= 0.172602E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6627E+04 1.7374E+01 1.3021E+02 C 19638 BOND = 8424.5004 ANGLE = 22185.9264 DIHED = 32481.7545 VDWAALS = -24142.3077 EEL = -191091.3727 EGB = -62532.6891 1-4 VDW = 10684.5627 1-4 EEL = 146366.7146 RESTRAINT = 0.0000 ESURF = 996.2044 minimization completed, ENE= -.56626706E+05 RMS= 0.173742E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6496E+04 1.7380E+01 1.3266E+02 C 45957 BOND = 8439.2134 ANGLE = 22311.7105 DIHED = 32418.8699 VDWAALS = -24097.5438 EEL = -190964.3792 EGB = -62768.2802 1-4 VDW = 10711.2664 1-4 EEL = 146455.7295 RESTRAINT = 0.0000 ESURF = 997.4362 minimization completed, ENE= -.56495977E+05 RMS= 0.173805E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6580E+04 1.7347E+01 1.1691E+02 C 27083 BOND = 8507.4218 ANGLE = 21996.8065 DIHED = 32372.1939 VDWAALS = -23977.3633 EEL = -190698.4355 EGB = -62879.7759 1-4 VDW = 10727.7151 1-4 EEL = 146376.1407 RESTRAINT = 0.0000 ESURF = 995.2532 minimization completed, ENE= -.56580044E+05 RMS= 0.173468E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6465E+04 1.7381E+01 1.3775E+02 C 16120 BOND = 8396.8745 ANGLE = 22134.1374 DIHED = 32488.8774 VDWAALS = -24068.1323 EEL = -190887.4801 EGB = -62791.7737 1-4 VDW = 10765.9193 1-4 EEL = 146502.1395 RESTRAINT = 0.0000 ESURF = 994.4767 minimization completed, ENE= -.56464961E+05 RMS= 0.173810E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6440E+04 1.7318E+01 1.1759E+02 N 2310 BOND = 8359.8075 ANGLE = 22270.9505 DIHED = 32361.1932 VDWAALS = -24062.7076 EEL = -190787.5636 EGB = -62740.3417 1-4 VDW = 10838.0625 1-4 EEL = 146324.5477 RESTRAINT = 0.0000 ESURF = 995.7715 minimization completed, ENE= -.56440280E+05 RMS= 0.173179E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6645E+04 1.7347E+01 1.2544E+02 C 1696 BOND = 8504.3248 ANGLE = 22168.0848 DIHED = 32376.3201 VDWAALS = -24060.0217 EEL = -190517.9390 EGB = -62807.7141 1-4 VDW = 10682.4646 1-4 EEL = 146012.4435 RESTRAINT = 0.0000 ESURF = 997.4303 minimization completed, ENE= -.56644607E+05 RMS= 0.173466E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6439E+04 1.7394E+01 1.5050E+02 C 11853 BOND = 8484.7436 ANGLE = 22217.8552 DIHED = 32457.4223 VDWAALS = -24116.5424 EEL = -190722.4044 EGB = -62849.3510 1-4 VDW = 10681.1679 1-4 EEL = 146412.6980 RESTRAINT = 0.0000 ESURF = 995.3349 minimization completed, ENE= -.56439076E+05 RMS= 0.173939E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6778E+04 1.7300E+01 1.2742E+02 C 18421 BOND = 8481.0736 ANGLE = 22025.5956 DIHED = 32383.4663 VDWAALS = -24060.1273 EEL = -191098.7544 EGB = -62563.6570 1-4 VDW = 10759.5679 1-4 EEL = 146301.2385 RESTRAINT = 0.0000 ESURF = 994.0285 minimization completed, ENE= -.56777568E+05 RMS= 0.173000E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6539E+04 1.7268E+01 1.3077E+02 C 38098 BOND = 8508.0704 ANGLE = 22261.3411 DIHED = 32451.7276 VDWAALS = -24024.4470 EEL = -190678.8874 EGB = -62780.9457 1-4 VDW = 10654.8859 1-4 EEL = 146077.4170 RESTRAINT = 0.0000 ESURF = 991.6544 minimization completed, ENE= -.56539184E+05 RMS= 0.172679E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6754E+04 1.7318E+01 1.2767E+02 C 37078 BOND = 8431.4182 ANGLE = 22131.5010 DIHED = 32415.4392 VDWAALS = -24191.4354 EEL = -190864.1817 EGB = -62688.5702 1-4 VDW = 10735.8253 1-4 EEL = 146284.0393 RESTRAINT = 0.0000 ESURF = 991.8764 minimization completed, ENE= -.56754088E+05 RMS= 0.173183E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6836E+04 1.7245E+01 1.3900E+02 C 15164 BOND = 8360.8571 ANGLE = 22119.0391 DIHED = 32478.3852 VDWAALS = -24057.3894 EEL = -191026.4249 EGB = -62643.3540 1-4 VDW = 10784.0068 1-4 EEL = 146162.3758 RESTRAINT = 0.0000 ESURF = 986.5584 minimization completed, ENE= -.56835946E+05 RMS= 0.172449E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2829.95 ( 4.95% of Gen B) | Calc gb diag 14009.32 (24.50% of Gen B) | Calc gb off-diag 40345.83 (70.55% of Gen B) | Gen Born time 57185.12 (100.0% of Nonbo) | Nonbond force 57185.12 (100.0% of Force) | Bond/Angle/Dihedral 17.62 ( 0.03% of Force) | Force time 57202.77 (100.0% of Runmd) | Runmd Time 57202.77 (99.84% of Total) | Other 91.23 ( 0.16% of Total) | Total time 57294.13 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:31:27.419 on 10/17/2010 | Setup done at 07:31:30.543 on 10/17/2010 | Run done at 23:26:21.547 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:31:21 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.3 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.3 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6210E+04 1.7449E+01 1.2935E+02 CG 2981 BOND = 8664.7613 ANGLE = 22376.5756 DIHED = 32384.5070 VDWAALS = -24116.1770 EEL = -190462.7869 EGB = -62997.5867 1-4 VDW = 10689.6922 1-4 EEL = 146261.6569 RESTRAINT = 0.0000 ESURF = 989.6479 minimization completed, ENE= -.56209710E+05 RMS= 0.174489E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6393E+04 1.7389E+01 1.3078E+02 CD 36381 BOND = 8493.1844 ANGLE = 22303.2790 DIHED = 32467.8629 VDWAALS = -24101.7553 EEL = -190422.6103 EGB = -62864.7224 1-4 VDW = 10721.1507 1-4 EEL = 146020.5032 RESTRAINT = 0.0000 ESURF = 990.0087 minimization completed, ENE= -.56393099E+05 RMS= 0.173894E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6722E+04 1.7433E+01 1.3218E+02 CG 33390 BOND = 8345.6952 ANGLE = 22142.6419 DIHED = 32396.6645 VDWAALS = -24154.3971 EEL = -190528.3435 EGB = -62946.5658 1-4 VDW = 10799.6608 1-4 EEL = 146232.4324 RESTRAINT = 0.0000 ESURF = 989.7602 minimization completed, ENE= -.56722451E+05 RMS= 0.174331E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6644E+04 1.7325E+01 1.2184E+02 CA 39916 BOND = 8250.0818 ANGLE = 22307.5804 DIHED = 32420.2752 VDWAALS = -24224.9198 EEL = -190400.8596 EGB = -62935.1475 1-4 VDW = 10754.8343 1-4 EEL = 146197.6618 RESTRAINT = 0.0000 ESURF = 986.6974 minimization completed, ENE= -.56643796E+05 RMS= 0.173253E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6712E+04 1.7301E+01 1.4423E+02 C 2209 BOND = 8434.0475 ANGLE = 22298.8083 DIHED = 32352.1347 VDWAALS = -24048.7716 EEL = -190260.5723 EGB = -63161.7542 1-4 VDW = 10677.2526 1-4 EEL = 146005.7730 RESTRAINT = 0.0000 ESURF = 991.2355 minimization completed, ENE= -.56711846E+05 RMS= 0.173007E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6664E+04 1.7299E+01 1.3381E+02 C 28426 BOND = 8329.9112 ANGLE = 22267.9476 DIHED = 32393.1811 VDWAALS = -24102.1393 EEL = -191037.0367 EGB = -62482.0102 1-4 VDW = 10721.6303 1-4 EEL = 146257.2954 RESTRAINT = 0.0000 ESURF = 987.4089 minimization completed, ENE= -.56663812E+05 RMS= 0.172994E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6360E+04 1.7318E+01 1.2744E+02 CG 32969 BOND = 8464.8923 ANGLE = 22425.3398 DIHED = 32448.3486 VDWAALS = -24102.8888 EEL = -191079.9374 EGB = -62397.5123 1-4 VDW = 10640.5602 1-4 EEL = 146254.1096 RESTRAINT = 0.0000 ESURF = 986.7401 minimization completed, ENE= -.56360348E+05 RMS= 0.173178E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6468E+04 1.7355E+01 1.3138E+02 C 39625 BOND = 8443.2159 ANGLE = 22264.9869 DIHED = 32487.8673 VDWAALS = -24107.8043 EEL = -190801.8991 EGB = -62487.4955 1-4 VDW = 10707.9197 1-4 EEL = 146033.7355 RESTRAINT = 0.0000 ESURF = 991.7983 minimization completed, ENE= -.56467675E+05 RMS= 0.173547E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6712E+04 1.7322E+01 1.2810E+02 CG 4706 BOND = 8385.5661 ANGLE = 22125.9118 DIHED = 32396.6550 VDWAALS = -24091.2125 EEL = -190696.6480 EGB = -62681.2559 1-4 VDW = 10759.3308 1-4 EEL = 146103.5708 RESTRAINT = 0.0000 ESURF = 986.1011 minimization completed, ENE= -.56711981E+05 RMS= 0.173222E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6429E+04 1.7430E+01 1.5310E+02 CD 37114 BOND = 8442.2665 ANGLE = 22330.4513 DIHED = 32415.0603 VDWAALS = -24127.8786 EEL = -190849.6422 EGB = -62652.6197 1-4 VDW = 10720.3001 1-4 EEL = 146306.9962 RESTRAINT = 0.0000 ESURF = 986.1624 minimization completed, ENE= -.56428904E+05 RMS= 0.174295E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6598E+04 1.7384E+01 1.2732E+02 C 38280 BOND = 8422.8325 ANGLE = 22153.8433 DIHED = 32391.8329 VDWAALS = -24035.9548 EEL = -191127.9739 EGB = -62492.3484 1-4 VDW = 10778.6837 1-4 EEL = 146314.5929 RESTRAINT = 0.0000 ESURF = 996.1370 minimization completed, ENE= -.56598355E+05 RMS= 0.173836E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6655E+04 1.7387E+01 1.1968E+02 N 46477 BOND = 8417.9114 ANGLE = 22187.3427 DIHED = 32461.5160 VDWAALS = -24009.4282 EEL = -190978.4220 EGB = -62788.3598 1-4 VDW = 10674.1457 1-4 EEL = 146382.3520 RESTRAINT = 0.0000 ESURF = 997.4664 minimization completed, ENE= -.56655476E+05 RMS= 0.173871E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6709E+04 1.7293E+01 1.2700E+02 CD 46087 BOND = 8238.5117 ANGLE = 22412.6598 DIHED = 32344.6043 VDWAALS = -24005.7691 EEL = -190784.9666 EGB = -62884.1419 1-4 VDW = 10683.5710 1-4 EEL = 146289.9987 RESTRAINT = 0.0000 ESURF = 996.5870 minimization completed, ENE= -.56708945E+05 RMS= 0.172927E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6475E+04 1.7403E+01 1.2414E+02 C 29282 BOND = 8581.9961 ANGLE = 22166.8536 DIHED = 32243.5750 VDWAALS = -24041.7850 EEL = -190744.8487 EGB = -62499.2573 1-4 VDW = 10729.1807 1-4 EEL = 146095.2806 RESTRAINT = 0.0000 ESURF = 993.8767 minimization completed, ENE= -.56475128E+05 RMS= 0.174034E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6421E+04 1.7273E+01 1.2154E+02 N 7892 BOND = 8359.7536 ANGLE = 22402.7428 DIHED = 32482.4181 VDWAALS = -24081.5940 EEL = -190878.4419 EGB = -62421.8874 1-4 VDW = 10665.5747 1-4 EEL = 146058.9353 RESTRAINT = 0.0000 ESURF = 991.1291 minimization completed, ENE= -.56421370E+05 RMS= 0.172728E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6408E+04 1.7364E+01 1.3313E+02 C 35923 BOND = 8471.7476 ANGLE = 22418.6834 DIHED = 32411.4694 VDWAALS = -24107.5553 EEL = -190838.3636 EGB = -62544.7306 1-4 VDW = 10687.9015 1-4 EEL = 146100.3067 RESTRAINT = 0.0000 ESURF = 992.6564 minimization completed, ENE= -.56407884E+05 RMS= 0.173640E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6197E+04 1.7461E+01 1.4426E+02 C 39748 BOND = 8644.0766 ANGLE = 22326.8919 DIHED = 32412.0143 VDWAALS = -24045.7722 EEL = -190916.0888 EGB = -62751.4984 1-4 VDW = 10805.2583 1-4 EEL = 146333.4592 RESTRAINT = 0.0000 ESURF = 994.8613 minimization completed, ENE= -.56196798E+05 RMS= 0.174608E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6509E+04 1.7358E+01 1.4001E+02 CD 35091 BOND = 8438.1125 ANGLE = 22346.6240 DIHED = 32417.2678 VDWAALS = -24135.7274 EEL = -191047.7853 EGB = -62535.3283 1-4 VDW = 10757.4441 1-4 EEL = 146258.8433 RESTRAINT = 0.0000 ESURF = 991.6207 minimization completed, ENE= -.56508929E+05 RMS= 0.173582E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6741E+04 1.7338E+01 1.2939E+02 CD 3751 BOND = 8403.5262 ANGLE = 22177.0423 DIHED = 32450.9212 VDWAALS = -24058.3005 EEL = -191368.8816 EGB = -62178.3158 1-4 VDW = 10704.7413 1-4 EEL = 146140.3193 RESTRAINT = 0.0000 ESURF = 988.1512 minimization completed, ENE= -.56740796E+05 RMS= 0.173377E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.7011E+04 1.7249E+01 1.2739E+02 C 25937 BOND = 8416.7372 ANGLE = 22128.3199 DIHED = 32314.7274 VDWAALS = -24195.4846 EEL = -191658.1479 EGB = -61862.8005 1-4 VDW = 10690.9896 1-4 EEL = 146165.4036 RESTRAINT = 0.0000 ESURF = 989.3095 minimization completed, ENE= -.57010946E+05 RMS= 0.172494E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6454E+04 1.7295E+01 1.4274E+02 C 28267 BOND = 8315.1752 ANGLE = 22356.7407 DIHED = 32565.4002 VDWAALS = -24062.8919 EEL = -191285.6885 EGB = -62234.1971 1-4 VDW = 10738.1527 1-4 EEL = 146161.6879 RESTRAINT = 0.0000 ESURF = 991.7932 minimization completed, ENE= -.56453828E+05 RMS= 0.172947E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6380E+04 1.7398E+01 1.3021E+02 N 22411 BOND = 8420.7249 ANGLE = 22243.9196 DIHED = 32429.6199 VDWAALS = -24089.7153 EEL = -191042.1651 EGB = -62437.3192 1-4 VDW = 10766.4932 1-4 EEL = 146339.9587 RESTRAINT = 0.0000 ESURF = 988.5202 minimization completed, ENE= -.56379963E+05 RMS= 0.173983E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6507E+04 1.7288E+01 1.4608E+02 CD 22582 BOND = 8353.1040 ANGLE = 22233.5464 DIHED = 32377.8371 VDWAALS = -24012.9690 EEL = -190695.0682 EGB = -62532.8460 1-4 VDW = 10732.5822 1-4 EEL = 146047.0555 RESTRAINT = 0.0000 ESURF = 989.7609 minimization completed, ENE= -.56506997E+05 RMS= 0.172882E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6564E+04 1.7376E+01 1.3709E+02 C 14398 BOND = 8480.4712 ANGLE = 22358.6398 DIHED = 32266.6496 VDWAALS = -24032.9700 EEL = -190892.4214 EGB = -62589.4331 1-4 VDW = 10724.5796 1-4 EEL = 146128.3378 RESTRAINT = 0.0000 ESURF = 992.2817 minimization completed, ENE= -.56563865E+05 RMS= 0.173764E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6824E+04 1.7277E+01 1.2878E+02 C 26412 BOND = 8376.6994 ANGLE = 22079.7940 DIHED = 32407.2778 VDWAALS = -24118.6120 EEL = -190523.3102 EGB = -62861.9236 1-4 VDW = 10711.4650 1-4 EEL = 146113.3767 RESTRAINT = 0.0000 ESURF = 991.6976 minimization completed, ENE= -.56823535E+05 RMS= 0.172768E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2785.72 ( 4.80% of Gen B) | Calc gb diag 13555.72 (23.34% of Gen B) | Calc gb off-diag 41748.81 (71.87% of Gen B) | Gen Born time 58090.56 (100.0% of Nonbo) | Nonbond force 58090.56 (100.0% of Force) | Bond/Angle/Dihedral 16.46 ( 0.03% of Force) | Force time 58107.05 (100.0% of Runmd) | Runmd Time 58107.05 (99.85% of Total) | Other 86.37 ( 0.15% of Total) | Total time 58193.54 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:31:21.449 on 10/17/2010 | Setup done at 07:31:24.724 on 10/17/2010 | Run done at 23:41:14.990 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:31:13 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.2 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.2 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6327E+04 1.7444E+01 1.2441E+02 C 27940 BOND = 8488.8800 ANGLE = 22280.2271 DIHED = 32409.2873 VDWAALS = -24073.7587 EEL = -190097.1290 EGB = -63344.6184 1-4 VDW = 10755.3816 1-4 EEL = 146266.4014 RESTRAINT = 0.0000 ESURF = 988.0505 minimization completed, ENE= -.56327278E+05 RMS= 0.174439E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6720E+04 1.7263E+01 1.2825E+02 C 2244 BOND = 8319.1900 ANGLE = 22259.6785 DIHED = 32371.9897 VDWAALS = -24267.3917 EEL = -190247.5262 EGB = -63028.9550 1-4 VDW = 10694.2063 1-4 EEL = 146191.6822 RESTRAINT = 0.0000 ESURF = 987.5330 minimization completed, ENE= -.56719593E+05 RMS= 0.172628E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6540E+04 1.7384E+01 1.3451E+02 C 3552 BOND = 8442.4783 ANGLE = 22123.3572 DIHED = 32334.6936 VDWAALS = -24079.1911 EEL = -190698.5582 EGB = -62859.0020 1-4 VDW = 10764.8520 1-4 EEL = 146447.1457 RESTRAINT = 0.0000 ESURF = 984.6090 minimization completed, ENE= -.56539616E+05 RMS= 0.173836E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6636E+04 1.7247E+01 1.2815E+02 C 23302 BOND = 8307.5441 ANGLE = 22189.7497 DIHED = 32350.5269 VDWAALS = -24112.5218 EEL = -190577.9807 EGB = -62904.3818 1-4 VDW = 10740.1181 1-4 EEL = 146386.1032 RESTRAINT = 0.0000 ESURF = 984.8545 minimization completed, ENE= -.56635988E+05 RMS= 0.172471E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6665E+04 1.7302E+01 1.3396E+02 CG 12739 BOND = 8545.9433 ANGLE = 22180.2752 DIHED = 32318.0787 VDWAALS = -24197.7181 EEL = -190507.3871 EGB = -62933.7205 1-4 VDW = 10733.3769 1-4 EEL = 146209.3407 RESTRAINT = 0.0000 ESURF = 986.4598 minimization completed, ENE= -.56665351E+05 RMS= 0.173018E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6687E+04 1.7276E+01 1.4173E+02 CZ 34760 BOND = 8425.6663 ANGLE = 22183.9224 DIHED = 32344.0066 VDWAALS = -24198.8758 EEL = -190397.1453 EGB = -63036.3072 1-4 VDW = 10773.8550 1-4 EEL = 146230.3497 RESTRAINT = 0.0000 ESURF = 987.1459 minimization completed, ENE= -.56687382E+05 RMS= 0.172760E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6760E+04 1.7245E+01 1.2322E+02 C 39732 BOND = 8349.7925 ANGLE = 22193.6441 DIHED = 32308.9257 VDWAALS = -24222.7827 EEL = -190834.0619 EGB = -62695.9305 1-4 VDW = 10750.9830 1-4 EEL = 146402.8968 RESTRAINT = 0.0000 ESURF = 986.4101 minimization completed, ENE= -.56760123E+05 RMS= 0.172450E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6288E+04 1.7401E+01 1.1986E+02 C 21334 BOND = 8396.3878 ANGLE = 22287.1687 DIHED = 32608.9118 VDWAALS = -24170.5456 EEL = -190634.1451 EGB = -62803.7060 1-4 VDW = 10737.0041 1-4 EEL = 146303.3105 RESTRAINT = 0.0000 ESURF = 987.9215 minimization completed, ENE= -.56287692E+05 RMS= 0.174013E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6536E+04 1.7347E+01 1.2286E+02 C 33670 BOND = 8384.8747 ANGLE = 22265.2652 DIHED = 32484.5831 VDWAALS = -24212.4782 EEL = -190518.9409 EGB = -62881.0016 1-4 VDW = 10746.5685 1-4 EEL = 146206.9058 RESTRAINT = 0.0000 ESURF = 987.7478 minimization completed, ENE= -.56536475E+05 RMS= 0.173466E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6401E+04 1.7381E+01 1.2736E+02 CA 43781 BOND = 8372.3220 ANGLE = 22294.8178 DIHED = 32422.5482 VDWAALS = -24050.1950 EEL = -190537.2621 EGB = -63052.0521 1-4 VDW = 10823.0871 1-4 EEL = 146336.5112 RESTRAINT = 0.0000 ESURF = 988.8990 minimization completed, ENE= -.56401324E+05 RMS= 0.173809E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6518E+04 1.7323E+01 1.4002E+02 N 24513 BOND = 8300.6062 ANGLE = 22559.3885 DIHED = 32321.7557 VDWAALS = -24081.6056 EEL = -190851.8937 EGB = -62548.0623 1-4 VDW = 10720.7706 1-4 EEL = 146071.0483 RESTRAINT = 0.0000 ESURF = 990.4458 minimization completed, ENE= -.56517547E+05 RMS= 0.173232E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6742E+04 1.7295E+01 1.3186E+02 C 33896 BOND = 8439.6316 ANGLE = 22269.6493 DIHED = 32278.1675 VDWAALS = -24199.4963 EEL = -190430.9327 EGB = -62921.5679 1-4 VDW = 10763.5335 1-4 EEL = 146070.1249 RESTRAINT = 0.0000 ESURF = 988.5106 minimization completed, ENE= -.56742379E+05 RMS= 0.172947E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6570E+04 1.7445E+01 1.2237E+02 C 40662 BOND = 8500.8394 ANGLE = 22190.5502 DIHED = 32375.7379 VDWAALS = -24132.2590 EEL = -190581.0817 EGB = -62965.8559 1-4 VDW = 10671.0152 1-4 EEL = 146383.1715 RESTRAINT = 0.0000 ESURF = 988.3582 minimization completed, ENE= -.56569524E+05 RMS= 0.174450E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6545E+04 1.7446E+01 1.4438E+02 CD 13609 BOND = 8435.9099 ANGLE = 22252.9129 DIHED = 32411.2302 VDWAALS = -24179.5969 EEL = -190927.9605 EGB = -62715.1824 1-4 VDW = 10775.8183 1-4 EEL = 146411.6315 RESTRAINT = 0.0000 ESURF = 989.7443 minimization completed, ENE= -.56545493E+05 RMS= 0.174463E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6607E+04 1.7342E+01 1.2691E+02 C 2115 BOND = 8474.5661 ANGLE = 22175.9634 DIHED = 32398.8836 VDWAALS = -24203.3855 EEL = -190601.1775 EGB = -62981.9809 1-4 VDW = 10770.8215 1-4 EEL = 146367.6438 RESTRAINT = 0.0000 ESURF = 991.8684 minimization completed, ENE= -.56606797E+05 RMS= 0.173423E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6478E+04 1.7338E+01 1.3778E+02 C 7599 BOND = 8407.0318 ANGLE = 22324.3024 DIHED = 32375.2350 VDWAALS = -24099.1977 EEL = -190268.7152 EGB = -63174.5893 1-4 VDW = 10724.1204 1-4 EEL = 146245.1008 RESTRAINT = 0.0000 ESURF = 988.8997 minimization completed, ENE= -.56477812E+05 RMS= 0.173377E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6736E+04 1.7337E+01 1.3013E+02 C 23661 BOND = 8375.0049 ANGLE = 22032.0421 DIHED = 32469.6309 VDWAALS = -24198.2947 EEL = -190547.4506 EGB = -63078.8736 1-4 VDW = 10769.8537 1-4 EEL = 146452.9400 RESTRAINT = 0.0000 ESURF = 988.7191 minimization completed, ENE= -.56736428E+05 RMS= 0.173373E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6530E+04 1.7414E+01 1.2596E+02 CA 13105 BOND = 8459.9057 ANGLE = 22244.7375 DIHED = 32480.3144 VDWAALS = -24128.8470 EEL = -190866.6586 EGB = -62693.9896 1-4 VDW = 10751.4124 1-4 EEL = 146234.9739 RESTRAINT = 0.0000 ESURF = 988.2982 minimization completed, ENE= -.56529853E+05 RMS= 0.174139E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6651E+04 1.7353E+01 1.5135E+02 CG 32301 BOND = 8525.7570 ANGLE = 22238.1927 DIHED = 32436.0349 VDWAALS = -24114.5867 EEL = -190934.1835 EGB = -62540.9556 1-4 VDW = 10688.9589 1-4 EEL = 146058.0321 RESTRAINT = 0.0000 ESURF = 992.0276 minimization completed, ENE= -.56650723E+05 RMS= 0.173529E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6599E+04 1.7306E+01 1.2631E+02 C 34979 BOND = 8512.2051 ANGLE = 22208.1276 DIHED = 32401.8852 VDWAALS = -24056.2082 EEL = -191476.6955 EGB = -62224.1118 1-4 VDW = 10804.9191 1-4 EEL = 146234.7076 RESTRAINT = 0.0000 ESURF = 995.8271 minimization completed, ENE= -.56599344E+05 RMS= 0.173062E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6832E+04 1.7337E+01 1.3429E+02 C 43719 BOND = 8462.6661 ANGLE = 22172.0604 DIHED = 32429.5418 VDWAALS = -24122.8244 EEL = -191291.6953 EGB = -62344.2136 1-4 VDW = 10640.4464 1-4 EEL = 146229.7838 RESTRAINT = 0.0000 ESURF = 991.8551 minimization completed, ENE= -.56832380E+05 RMS= 0.173369E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6555E+04 1.7315E+01 1.1985E+02 C 5339 BOND = 8345.8925 ANGLE = 22312.4995 DIHED = 32363.3494 VDWAALS = -24041.4339 EEL = -190924.1821 EGB = -62508.1954 1-4 VDW = 10729.1235 1-4 EEL = 146175.2179 RESTRAINT = 0.0000 ESURF = 992.7778 minimization completed, ENE= -.56554951E+05 RMS= 0.173153E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6588E+04 1.7210E+01 1.2059E+02 C 30586 BOND = 8331.2241 ANGLE = 22387.7723 DIHED = 32412.2863 VDWAALS = -24025.1203 EEL = -190662.7239 EGB = -62904.8147 1-4 VDW = 10737.4128 1-4 EEL = 146142.3831 RESTRAINT = 0.0000 ESURF = 993.2710 minimization completed, ENE= -.56588309E+05 RMS= 0.172098E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6191E+04 1.7481E+01 1.1932E+02 C 18169 BOND = 8474.4991 ANGLE = 22339.1816 DIHED = 32376.8933 VDWAALS = -24036.0970 EEL = -190957.1336 EGB = -62627.0228 1-4 VDW = 10816.9338 1-4 EEL = 146430.3550 RESTRAINT = 0.0000 ESURF = 991.6889 minimization completed, ENE= -.56190702E+05 RMS= 0.174813E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6381E+04 1.7367E+01 1.3238E+02 CD 16823 BOND = 8449.5527 ANGLE = 22398.3265 DIHED = 32360.9141 VDWAALS = -24027.5554 EEL = -190352.5718 EGB = -63023.2032 1-4 VDW = 10650.9168 1-4 EEL = 146170.6157 RESTRAINT = 0.0000 ESURF = 992.1822 minimization completed, ENE= -.56380822E+05 RMS= 0.173674E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2841.24 ( 4.96% of Gen B) | Calc gb diag 14018.16 (24.47% of Gen B) | Calc gb off-diag 40426.59 (70.57% of Gen B) | Gen Born time 57286.00 (100.0% of Nonbo) | Nonbond force 57286.00 (100.0% of Force) | Bond/Angle/Dihedral 16.80 ( 0.03% of Force) | Force time 57302.83 (100.0% of Runmd) | Runmd Time 57302.83 (99.84% of Total) | Other 90.12 ( 0.16% of Total) | Total time 57393.07 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:31:13.959 on 10/17/2010 | Setup done at 07:31:17.599 on 10/17/2010 | Run done at 23:27:47.029 on 10/17/2010 | wallclock() was called 909 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/17/2010 at 07:31:07 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _rec.out.1 |INPCRD: 1XCK_hept_noWAT_noA.inpcrd | PARM: 1XCK_hept_noWAT_noA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _rec.mdcrd.1 | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, idecomp=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, ncyc=0, igb=5, saltcon=0.0, intdiel=1, extdiel=78.3, gbsa=2, surften=0.0072, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 10/15/10 Time = 23:14:13 NATOM = 47010 NTYPES = 14 NBONH = 23874 MBONA = 23304 NTHETH = 54534 MTHETA = 31470 NPHIH = 101790 MPHIA = 74094 NHPARM = 0 NPARM = 0 NNB = 259236 NRES = 3144 NBONA = 23304 NTHETA = 31470 NPHIA = 74094 NUMBND = 35 NUMANG = 73 NPTRA = 43 NATYP = 26 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3385565 | Hollerith 144176 | Integer 6235186 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 51369 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 5, nsnb = 99999 ipol = 0, gbsa = 2, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES trajectory generated by ptraj minimizing coord set # 1 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6452E+04 1.7328E+01 1.3179E+02 CD 19209 BOND = 8450.9303 ANGLE = 22291.4798 DIHED = 32435.2065 VDWAALS = -24253.5332 EEL = -190622.8342 EGB = -62757.9546 1-4 VDW = 10765.5191 1-4 EEL = 146252.8313 RESTRAINT = 0.0000 ESURF = 986.3674 minimization completed, ENE= -.56451988E+05 RMS= 0.173280E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6702E+04 1.7285E+01 1.3650E+02 C 27926 BOND = 8396.4389 ANGLE = 22324.4101 DIHED = 32206.4408 VDWAALS = -24210.8196 EEL = -190680.2653 EGB = -62771.5153 1-4 VDW = 10759.6554 1-4 EEL = 146291.2339 RESTRAINT = 0.0000 ESURF = 982.3582 minimization completed, ENE= -.56702063E+05 RMS= 0.172847E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6534E+04 1.7312E+01 1.3109E+02 C 2420 BOND = 8495.4146 ANGLE = 22210.3812 DIHED = 32230.4807 VDWAALS = -24108.0786 EEL = -190160.7205 EGB = -63057.1894 1-4 VDW = 10725.5839 1-4 EEL = 146143.4625 RESTRAINT = 0.0000 ESURF = 986.9578 minimization completed, ENE= -.56533708E+05 RMS= 0.173116E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6752E+04 1.7307E+01 1.3144E+02 C 32132 BOND = 8350.1089 ANGLE = 22145.2578 DIHED = 32409.5769 VDWAALS = -24154.0292 EEL = -190458.6252 EGB = -63034.3635 1-4 VDW = 10703.3275 1-4 EEL = 146296.1245 RESTRAINT = 0.0000 ESURF = 990.2443 minimization completed, ENE= -.56752378E+05 RMS= 0.173065E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6553E+04 1.7391E+01 1.1777E+02 C 31859 BOND = 8355.0949 ANGLE = 22176.3474 DIHED = 32475.9183 VDWAALS = -24046.8347 EEL = -190637.6999 EGB = -62948.6060 1-4 VDW = 10767.0744 1-4 EEL = 146319.4877 RESTRAINT = 0.0000 ESURF = 986.3424 minimization completed, ENE= -.56552876E+05 RMS= 0.173907E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6409E+04 1.7336E+01 1.2420E+02 CD 5244 BOND = 8358.0797 ANGLE = 22230.6103 DIHED = 32314.5304 VDWAALS = -24068.8685 EEL = -190422.8041 EGB = -63031.3005 1-4 VDW = 10784.7213 1-4 EEL = 146438.0793 RESTRAINT = 0.0000 ESURF = 987.5203 minimization completed, ENE= -.56409432E+05 RMS= 0.173365E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6325E+04 1.7383E+01 1.2696E+02 C 4018 BOND = 8425.3740 ANGLE = 22385.5181 DIHED = 32434.9871 VDWAALS = -24059.2618 EEL = -190173.8900 EGB = -63271.5616 1-4 VDW = 10697.1969 1-4 EEL = 146249.5799 RESTRAINT = 0.0000 ESURF = 987.1628 minimization completed, ENE= -.56324895E+05 RMS= 0.173832E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6355E+04 1.7388E+01 1.1921E+02 CA 8237 BOND = 8561.1911 ANGLE = 22428.6209 DIHED = 32408.3438 VDWAALS = -24102.7860 EEL = -189961.2414 EGB = -63549.1181 1-4 VDW = 10655.4432 1-4 EEL = 146209.5271 RESTRAINT = 0.0000 ESURF = 994.5553 minimization completed, ENE= -.56355464E+05 RMS= 0.173885E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6768E+04 1.7265E+01 1.2194E+02 C 19593 BOND = 8423.7054 ANGLE = 22170.8565 DIHED = 32285.5013 VDWAALS = -24152.6604 EEL = -189917.5637 EGB = -63317.0897 1-4 VDW = 10666.9499 1-4 EEL = 146078.7980 RESTRAINT = 0.0000 ESURF = 993.4015 minimization completed, ENE= -.56768101E+05 RMS= 0.172649E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6387E+04 1.7372E+01 1.3584E+02 C 8539 BOND = 8340.3643 ANGLE = 22341.6501 DIHED = 32423.1251 VDWAALS = -24077.2168 EEL = -190354.1878 EGB = -63240.1556 1-4 VDW = 10768.4545 1-4 EEL = 146412.9432 RESTRAINT = 0.0000 ESURF = 998.1446 minimization completed, ENE= -.56386878E+05 RMS= 0.173718E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6455E+04 1.7351E+01 1.3667E+02 C 2244 BOND = 8393.4624 ANGLE = 22245.1705 DIHED = 32414.0856 VDWAALS = -24148.6413 EEL = -190418.3588 EGB = -63074.3462 1-4 VDW = 10793.3920 1-4 EEL = 146351.6224 RESTRAINT = 0.0000 ESURF = 988.3708 minimization completed, ENE= -.56455243E+05 RMS= 0.173515E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6678E+04 1.7277E+01 1.2986E+02 C 45890 BOND = 8417.5900 ANGLE = 22028.2653 DIHED = 32477.1274 VDWAALS = -24144.1917 EEL = -190385.9215 EGB = -63126.3235 1-4 VDW = 10734.4490 1-4 EEL = 146337.6811 RESTRAINT = 0.0000 ESURF = 983.3919 minimization completed, ENE= -.56677932E+05 RMS= 0.172774E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6557E+04 1.7314E+01 1.2315E+02 C 3508 BOND = 8404.8687 ANGLE = 22118.2506 DIHED = 32375.8613 VDWAALS = -24166.3860 EEL = -190265.1249 EGB = -63250.8903 1-4 VDW = 10771.3000 1-4 EEL = 146470.3852 RESTRAINT = 0.0000 ESURF = 984.8875 minimization completed, ENE= -.56556848E+05 RMS= 0.173144E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6339E+04 1.7346E+01 1.2534E+02 CG 2852 BOND = 8402.8302 ANGLE = 22467.6580 DIHED = 32376.2140 VDWAALS = -24171.2253 EEL = -189888.6938 EGB = -63442.9405 1-4 VDW = 10714.0467 1-4 EEL = 146218.3595 RESTRAINT = 0.0000 ESURF = 984.4177 minimization completed, ENE= -.56339333E+05 RMS= 0.173456E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6296E+04 1.7413E+01 1.4487E+02 C 8347 BOND = 8371.2596 ANGLE = 22333.5241 DIHED = 32381.0133 VDWAALS = -24133.6877 EEL = -189857.9655 EGB = -63297.8909 1-4 VDW = 10753.8549 1-4 EEL = 146171.9781 RESTRAINT = 0.0000 ESURF = 982.3614 minimization completed, ENE= -.56295553E+05 RMS= 0.174133E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6496E+04 1.7403E+01 1.3752E+02 N 9310 BOND = 8437.3452 ANGLE = 22333.2261 DIHED = 32470.5523 VDWAALS = -24276.3271 EEL = -190376.8353 EGB = -63049.1458 1-4 VDW = 10644.4385 1-4 EEL = 146340.1017 RESTRAINT = 0.0000 ESURF = 980.4061 minimization completed, ENE= -.56496238E+05 RMS= 0.174030E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6524E+04 1.7404E+01 1.2376E+02 C 4297 BOND = 8510.3291 ANGLE = 22127.9725 DIHED = 32428.0550 VDWAALS = -24112.9310 EEL = -190400.0742 EGB = -62942.2396 1-4 VDW = 10680.4897 1-4 EEL = 146199.2777 RESTRAINT = 0.0000 ESURF = 984.8733 minimization completed, ENE= -.56524248E+05 RMS= 0.174039E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6534E+04 1.7363E+01 1.3792E+02 C 5664 BOND = 8339.5129 ANGLE = 22400.0913 DIHED = 32458.0143 VDWAALS = -24140.3733 EEL = -190294.6406 EGB = -63237.0832 1-4 VDW = 10707.2067 1-4 EEL = 146250.5139 RESTRAINT = 0.0000 ESURF = 982.4642 minimization completed, ENE= -.56534294E+05 RMS= 0.173629E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6547E+04 1.7302E+01 1.1868E+02 CA 4739 BOND = 8365.2409 ANGLE = 22188.3142 DIHED = 32445.7290 VDWAALS = -24113.4885 EEL = -190331.9645 EGB = -63229.2494 1-4 VDW = 10723.6548 1-4 EEL = 146418.9531 RESTRAINT = 0.0000 ESURF = 985.5124 minimization completed, ENE= -.56547298E+05 RMS= 0.173023E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6416E+04 1.7433E+01 1.3574E+02 C 46367 BOND = 8363.1858 ANGLE = 22243.7590 DIHED = 32349.5592 VDWAALS = -24137.3176 EEL = -190104.9203 EGB = -63244.1311 1-4 VDW = 10854.6371 1-4 EEL = 146272.1179 RESTRAINT = 0.0000 ESURF = 987.3058 minimization completed, ENE= -.56415804E+05 RMS= 0.174333E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6730E+04 1.7315E+01 1.3414E+02 C 23321 BOND = 8391.1008 ANGLE = 22170.9047 DIHED = 32400.5843 VDWAALS = -24125.5118 EEL = -190530.7335 EGB = -63166.8801 1-4 VDW = 10769.0541 1-4 EEL = 146372.6413 RESTRAINT = 0.0000 ESURF = 989.3377 minimization completed, ENE= -.56729502E+05 RMS= 0.173146E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6439E+04 1.7426E+01 1.2312E+02 C 37078 BOND = 8414.8857 ANGLE = 22283.5447 DIHED = 32460.9695 VDWAALS = -24204.2905 EEL = -190353.7000 EGB = -63039.8617 1-4 VDW = 10807.0835 1-4 EEL = 146205.7809 RESTRAINT = 0.0000 ESURF = 986.3727 minimization completed, ENE= -.56439215E+05 RMS= 0.174263E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6775E+04 1.7276E+01 1.2705E+02 C 18662 BOND = 8388.3086 ANGLE = 21946.1550 DIHED = 32329.4834 VDWAALS = -24097.1366 EEL = -190318.2183 EGB = -63106.4018 1-4 VDW = 10772.8147 1-4 EEL = 146320.3614 RESTRAINT = 0.0000 ESURF = 989.1869 minimization completed, ENE= -.56775447E+05 RMS= 0.172757E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6398E+04 1.7328E+01 1.2916E+02 CD 8784 BOND = 8346.7453 ANGLE = 22291.3967 DIHED = 32463.8223 VDWAALS = -24128.9150 EEL = -190255.7131 EGB = -63070.9060 1-4 VDW = 10754.3096 1-4 EEL = 146211.6883 RESTRAINT = 0.0000 ESURF = 989.6621 minimization completed, ENE= -.56397910E+05 RMS= 0.173277E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.6772E+04 1.7327E+01 1.1913E+02 C 11343 BOND = 8402.4896 ANGLE = 22101.3761 DIHED = 32261.9395 VDWAALS = -24038.6442 EEL = -190256.6162 EGB = -63200.5132 1-4 VDW = 10719.0573 1-4 EEL = 146248.6325 RESTRAINT = 0.0000 ESURF = 990.3513 minimization completed, ENE= -.56771927E+05 RMS= 0.173274E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 2845.88 ( 4.97% of Gen B) | Calc gb diag 14039.14 (24.52% of Gen B) | Calc gb off-diag 40359.72 (70.50% of Gen B) | Gen Born time 57244.75 (100.0% of Nonbo) | Nonbond force 57244.75 (100.0% of Force) | Bond/Angle/Dihedral 16.09 ( 0.03% of Force) | Force time 57260.96 (100.0% of Runmd) | Runmd Time 57260.96 (99.85% of Total) | Other 87.92 ( 0.15% of Total) | Total time 57349.46 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:31:07.499 on 10/17/2010 | Setup done at 07:31:11.132 on 10/17/2010 | Run done at 23:26:56.957 on 10/17/2010 | wallclock() was called 909 times