------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/20/2010 at 00:30:19 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _lig.out.16 |INPCRD: 1XCK_chainA_MGATP_noWAT.inpcrd | PARM: 1XCK_chainA_MGATP_noWAT.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _lig.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 = 09/24/09 Time = 02:43:23 NATOM = 7879 NTYPES = 18 NBONH = 3991 MBONA = 3917 NTHETH = 9115 MTHETA = 5297 NPHIH = 17023 MPHIA = 12427 NHPARM = 0 NPARM = 0 NNB = 43422 NRES = 526 NBONA = 3917 NTHETA = 5297 NPHIA = 12427 NUMBND = 52 NUMANG = 108 NPTRA = 66 NATYP = 36 NPHB = 0 IFBOX = 0 NMXRS = 43 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 567848 | Hollerith 24165 | Integer 1061772 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 8678 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 -1.0709E+04 1.7211E+01 1.1283E+02 PA 7846 BOND = 1412.1270 ANGLE = 3718.0811 DIHED = 5409.8740 VDWAALS = -3829.4966 EEL = -34706.1356 EGB = -8018.2034 1-4 VDW = 1807.7197 1-4 EEL = 23308.4388 RESTRAINT = 0.0000 ESURF = 188.9684 minimization completed, ENE= -.10708627E+05 RMS= 0.172107E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0693E+04 1.7220E+01 1.3345E+02 C 1103 BOND = 1413.7835 ANGLE = 3756.7307 DIHED = 5387.9641 VDWAALS = -3842.8180 EEL = -34716.6315 EGB = -8031.9086 1-4 VDW = 1790.7544 1-4 EEL = 23360.6779 RESTRAINT = 0.0000 ESURF = 188.4427 minimization completed, ENE= -.10693005E+05 RMS= 0.172202E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0810E+04 1.7172E+01 9.9892E+01 CD1 2961 BOND = 1366.2446 ANGLE = 3692.3199 DIHED = 5380.0729 VDWAALS = -3915.7868 EEL = -34855.2401 EGB = -7846.4600 1-4 VDW = 1804.7006 1-4 EEL = 23377.7507 RESTRAINT = 0.0000 ESURF = 186.0718 minimization completed, ENE= -.10810326E+05 RMS= 0.171718E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0579E+04 1.7552E+01 1.1596E+02 N 5287 BOND = 1466.0702 ANGLE = 3776.8615 DIHED = 5387.8714 VDWAALS = -3884.7952 EEL = -34442.9952 EGB = -8151.7562 1-4 VDW = 1787.1160 1-4 EEL = 23293.2026 RESTRAINT = 0.0000 ESURF = 189.2624 minimization completed, ENE= -.10579162E+05 RMS= 0.175521E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0702E+04 1.7630E+01 1.1182E+02 C 4270 BOND = 1413.7887 ANGLE = 3735.3532 DIHED = 5390.5671 VDWAALS = -3870.7339 EEL = -34772.9230 EGB = -7983.8338 1-4 VDW = 1799.6026 1-4 EEL = 23398.1763 RESTRAINT = 0.0000 ESURF = 188.0559 minimization completed, ENE= -.10701947E+05 RMS= 0.176300E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0709E+04 1.7374E+01 1.1712E+02 C 4484 BOND = 1417.2731 ANGLE = 3825.7956 DIHED = 5381.2743 VDWAALS = -3877.9296 EEL = -34746.5891 EGB = -8076.2029 1-4 VDW = 1794.2059 1-4 EEL = 23382.6728 RESTRAINT = 0.0000 ESURF = 190.1991 minimization completed, ENE= -.10709301E+05 RMS= 0.173737E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0647E+04 1.7224E+01 1.1306E+02 C 6379 BOND = 1395.0089 ANGLE = 3776.1392 DIHED = 5425.3367 VDWAALS = -3894.8638 EEL = -34559.9196 EGB = -8065.9259 1-4 VDW = 1800.6644 1-4 EEL = 23290.1799 RESTRAINT = 0.0000 ESURF = 186.6202 minimization completed, ENE= -.10646760E+05 RMS= 0.172242E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0804E+04 1.7200E+01 1.2977E+02 C 2285 BOND = 1410.1170 ANGLE = 3609.3438 DIHED = 5364.0921 VDWAALS = -3805.9557 EEL = -34977.0183 EGB = -7916.3618 1-4 VDW = 1833.4877 1-4 EEL = 23490.0498 RESTRAINT = 0.0000 ESURF = 187.8783 minimization completed, ENE= -.10804367E+05 RMS= 0.171995E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0738E+04 1.7221E+01 1.2603E+02 CZ 6437 BOND = 1427.3212 ANGLE = 3676.4864 DIHED = 5398.8969 VDWAALS = -3877.6100 EEL = -34659.9809 EGB = -8119.8964 1-4 VDW = 1803.7001 1-4 EEL = 23423.0250 RESTRAINT = 0.0000 ESURF = 190.3179 minimization completed, ENE= -.10737740E+05 RMS= 0.172207E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0760E+04 1.7233E+01 1.1528E+02 C 7281 BOND = 1395.7490 ANGLE = 3647.0953 DIHED = 5410.7743 VDWAALS = -3895.0795 EEL = -34529.6720 EGB = -8173.0799 1-4 VDW = 1818.3252 1-4 EEL = 23376.5334 RESTRAINT = 0.0000 ESURF = 188.9469 minimization completed, ENE= -.10760407E+05 RMS= 0.172332E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0678E+04 1.7307E+01 1.2279E+02 C 5475 BOND = 1445.6852 ANGLE = 3768.3666 DIHED = 5424.0785 VDWAALS = -3849.3068 EEL = -34556.8939 EGB = -8158.9856 1-4 VDW = 1779.9746 1-4 EEL = 23277.2841 RESTRAINT = 0.0000 ESURF = 191.6573 minimization completed, ENE= -.10678140E+05 RMS= 0.173068E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0685E+04 1.7455E+01 1.1010E+02 C 372 BOND = 1434.8442 ANGLE = 3683.7426 DIHED = 5424.2780 VDWAALS = -3831.3230 EEL = -34745.8841 EGB = -8070.4733 1-4 VDW = 1806.8259 1-4 EEL = 23423.2338 RESTRAINT = 0.0000 ESURF = 190.0695 minimization completed, ENE= -.10684687E+05 RMS= 0.174554E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0639E+04 1.7251E+01 1.1592E+02 C 1278 BOND = 1379.9823 ANGLE = 3755.0599 DIHED = 5427.7941 VDWAALS = -3830.9776 EEL = -34649.8673 EGB = -8087.9419 1-4 VDW = 1818.4513 1-4 EEL = 23359.7305 RESTRAINT = 0.0000 ESURF = 188.9307 minimization completed, ENE= -.10638838E+05 RMS= 0.172515E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0645E+04 1.7438E+01 1.2227E+02 CA 2223 BOND = 1404.1510 ANGLE = 3782.5241 DIHED = 5446.0645 VDWAALS = -3882.5776 EEL = -34829.2587 EGB = -7944.0128 1-4 VDW = 1802.5683 1-4 EEL = 23388.0824 RESTRAINT = 0.0000 ESURF = 187.9434 minimization completed, ENE= -.10644515E+05 RMS= 0.174385E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0661E+04 1.7257E+01 1.0872E+02 CD 5312 BOND = 1411.5482 ANGLE = 3673.7153 DIHED = 5423.4911 VDWAALS = -3847.6690 EEL = -34705.9060 EGB = -7956.3293 1-4 VDW = 1814.4019 1-4 EEL = 23338.2938 RESTRAINT = 0.0000 ESURF = 187.1832 minimization completed, ENE= -.10661271E+05 RMS= 0.172569E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0654E+04 1.7438E+01 1.2391E+02 C 4407 BOND = 1437.6434 ANGLE = 3782.6051 DIHED = 5463.6527 VDWAALS = -3868.4304 EEL = -34713.3266 EGB = -8034.3128 1-4 VDW = 1793.2287 1-4 EEL = 23298.5755 RESTRAINT = 0.0000 ESURF = 186.8242 minimization completed, ENE= -.10653540E+05 RMS= 0.174376E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0669E+04 1.7538E+01 1.1437E+02 C 3107 BOND = 1433.9421 ANGLE = 3809.2987 DIHED = 5374.1927 VDWAALS = -3918.0361 EEL = -34782.3620 EGB = -7979.7304 1-4 VDW = 1814.6347 1-4 EEL = 23393.7809 RESTRAINT = 0.0000 ESURF = 185.3239 minimization completed, ENE= -.10668955E+05 RMS= 0.175377E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0617E+04 1.7444E+01 1.3690E+02 CD 1420 BOND = 1445.2186 ANGLE = 3744.7485 DIHED = 5411.5486 VDWAALS = -3849.3428 EEL = -34646.3235 EGB = -8050.3229 1-4 VDW = 1808.9636 1-4 EEL = 23332.5667 RESTRAINT = 0.0000 ESURF = 186.3717 minimization completed, ENE= -.10616572E+05 RMS= 0.174441E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0706E+04 1.7254E+01 1.1694E+02 C 1311 BOND = 1428.3251 ANGLE = 3711.2361 DIHED = 5415.0962 VDWAALS = -3883.0220 EEL = -34757.4676 EGB = -8028.7275 1-4 VDW = 1825.0226 1-4 EEL = 23393.7654 RESTRAINT = 0.0000 ESURF = 189.9737 minimization completed, ENE= -.10705798E+05 RMS= 0.172535E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0665E+04 1.7437E+01 1.1748E+02 CD 2598 BOND = 1444.0595 ANGLE = 3779.7579 DIHED = 5396.9271 VDWAALS = -3927.8555 EEL = -34778.3912 EGB = -8022.0091 1-4 VDW = 1804.2554 1-4 EEL = 23449.5834 RESTRAINT = 0.0000 ESURF = 188.4534 minimization completed, ENE= -.10665219E+05 RMS= 0.174369E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0644E+04 1.7400E+01 1.1216E+02 C 2879 BOND = 1457.9100 ANGLE = 3844.3432 DIHED = 5421.2255 VDWAALS = -3943.1818 EEL = -34768.6109 EGB = -7966.5325 1-4 VDW = 1784.5384 1-4 EEL = 23339.4616 RESTRAINT = 0.0000 ESURF = 187.2965 minimization completed, ENE= -.10643550E+05 RMS= 0.174002E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0645E+04 1.7149E+01 1.1333E+02 C 3754 BOND = 1446.5053 ANGLE = 3785.0575 DIHED = 5417.2077 VDWAALS = -3872.0429 EEL = -34830.9303 EGB = -7877.8607 1-4 VDW = 1783.3034 1-4 EEL = 23315.9616 RESTRAINT = 0.0000 ESURF = 188.0497 minimization completed, ENE= -.10644749E+05 RMS= 0.171494E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0744E+04 1.7205E+01 1.0271E+02 C 6715 BOND = 1425.8002 ANGLE = 3708.0527 DIHED = 5447.2410 VDWAALS = -3892.5098 EEL = -34708.1665 EGB = -8000.4226 1-4 VDW = 1766.0080 1-4 EEL = 23322.2247 RESTRAINT = 0.0000 ESURF = 187.7587 minimization completed, ENE= -.10744014E+05 RMS= 0.172047E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0657E+04 1.7204E+01 1.1803E+02 CG 5359 BOND = 1398.8029 ANGLE = 3840.6839 DIHED = 5394.0966 VDWAALS = -3922.8690 EEL = -34740.9008 EGB = -7905.3394 1-4 VDW = 1787.2417 1-4 EEL = 23305.4691 RESTRAINT = 0.0000 ESURF = 186.2452 minimization completed, ENE= -.10656570E+05 RMS= 0.172036E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0718E+04 1.7511E+01 1.2113E+02 CG 2732 BOND = 1455.6225 ANGLE = 3686.4604 DIHED = 5376.1935 VDWAALS = -3842.6695 EEL = -34808.6418 EGB = -7928.9399 1-4 VDW = 1822.3762 1-4 EEL = 23334.9410 RESTRAINT = 0.0000 ESURF = 186.7506 minimization completed, ENE= -.10717907E+05 RMS= 0.175107E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0726E+04 1.7338E+01 1.3534E+02 CG 5392 BOND = 1406.4110 ANGLE = 3757.4823 DIHED = 5385.8806 VDWAALS = -3878.1294 EEL = -34896.0440 EGB = -7958.9395 1-4 VDW = 1824.3048 1-4 EEL = 23445.6626 RESTRAINT = 0.0000 ESURF = 187.8045 minimization completed, ENE= -.10725567E+05 RMS= 0.173375E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0658E+04 1.7404E+01 1.1431E+02 N 4737 BOND = 1407.9284 ANGLE = 3748.3880 DIHED = 5418.0261 VDWAALS = -3856.3554 EEL = -34553.6869 EGB = -8084.4658 1-4 VDW = 1765.9961 1-4 EEL = 23308.8893 RESTRAINT = 0.0000 ESURF = 187.5873 minimization completed, ENE= -.10657693E+05 RMS= 0.174041E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0517E+04 1.7366E+01 1.1137E+02 CG 7153 BOND = 1405.2678 ANGLE = 3844.5149 DIHED = 5440.0604 VDWAALS = -3839.5816 EEL = -34610.7149 EGB = -8103.0957 1-4 VDW = 1811.2088 1-4 EEL = 23346.4626 RESTRAINT = 0.0000 ESURF = 188.3900 minimization completed, ENE= -.10517488E+05 RMS= 0.173660E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0601E+04 1.7291E+01 1.1335E+02 CA 2911 BOND = 1395.7791 ANGLE = 3807.8659 DIHED = 5403.7422 VDWAALS = -3813.8754 EEL = -34777.6231 EGB = -7989.6693 1-4 VDW = 1828.1196 1-4 EEL = 23358.1529 RESTRAINT = 0.0000 ESURF = 186.4057 minimization completed, ENE= -.10601102E+05 RMS= 0.172910E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0754E+04 1.7175E+01 1.1520E+02 C 5266 BOND = 1348.8224 ANGLE = 3677.9439 DIHED = 5465.5841 VDWAALS = -3863.3130 EEL = -35001.6727 EGB = -7745.0338 1-4 VDW = 1811.8952 1-4 EEL = 23366.2589 RESTRAINT = 0.0000 ESURF = 185.9646 minimization completed, ENE= -.10753550E+05 RMS= 0.171751E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0724E+04 1.7344E+01 1.1886E+02 CG 961 BOND = 1419.3230 ANGLE = 3706.0309 DIHED = 5401.8071 VDWAALS = -3859.2002 EEL = -34888.0220 EGB = -7865.7234 1-4 VDW = 1815.9461 1-4 EEL = 23357.3360 RESTRAINT = 0.0000 ESURF = 188.0420 minimization completed, ENE= -.10724460E+05 RMS= 0.173438E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0782E+04 1.7351E+01 1.1464E+02 CD2 7114 BOND = 1417.9684 ANGLE = 3667.2511 DIHED = 5413.6322 VDWAALS = -3836.5946 EEL = -34782.3931 EGB = -7967.1281 1-4 VDW = 1780.5813 1-4 EEL = 23336.5666 RESTRAINT = 0.0000 ESURF = 188.2082 minimization completed, ENE= -.10781908E+05 RMS= 0.173513E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0564E+04 1.7368E+01 1.2734E+02 CG 5980 BOND = 1409.7407 ANGLE = 3815.2839 DIHED = 5435.6417 VDWAALS = -3860.8117 EEL = -34623.4143 EGB = -8066.2849 1-4 VDW = 1794.7281 1-4 EEL = 23342.3837 RESTRAINT = 0.0000 ESURF = 188.4332 minimization completed, ENE= -.10564300E+05 RMS= 0.173682E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0725E+04 1.7194E+01 1.0750E+02 C 5956 BOND = 1389.7552 ANGLE = 3748.0700 DIHED = 5437.0068 VDWAALS = -3870.0549 EEL = -34767.5628 EGB = -7953.1496 1-4 VDW = 1815.3063 1-4 EEL = 23288.5203 RESTRAINT = 0.0000 ESURF = 187.4126 minimization completed, ENE= -.10724696E+05 RMS= 0.171941E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0788E+04 1.6981E+01 1.0827E+02 C 2514 BOND = 1395.8573 ANGLE = 3742.8796 DIHED = 5382.4083 VDWAALS = -3849.5688 EEL = -34750.7290 EGB = -7952.2829 1-4 VDW = 1760.9926 1-4 EEL = 23292.3734 RESTRAINT = 0.0000 ESURF = 189.9246 minimization completed, ENE= -.10788145E+05 RMS= 0.169809E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0687E+04 1.7113E+01 9.9601E+01 C 512 BOND = 1384.4356 ANGLE = 3673.3660 DIHED = 5489.5267 VDWAALS = -3890.1386 EEL = -34971.7590 EGB = -7825.7826 1-4 VDW = 1821.1269 1-4 EEL = 23445.7631 RESTRAINT = 0.0000 ESURF = 186.6464 minimization completed, ENE= -.10686816E+05 RMS= 0.171129E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0494E+04 1.7658E+01 1.1782E+02 C 2378 BOND = 1451.9137 ANGLE = 3804.7817 DIHED = 5459.6026 VDWAALS = -3853.9403 EEL = -34681.2803 EGB = -8000.1518 1-4 VDW = 1816.2721 1-4 EEL = 23318.5429 RESTRAINT = 0.0000 ESURF = 190.1612 minimization completed, ENE= -.10494098E+05 RMS= 0.176583E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0779E+04 1.7214E+01 1.1329E+02 CA 6455 BOND = 1419.1280 ANGLE = 3677.8923 DIHED = 5409.3179 VDWAALS = -3890.2113 EEL = -34767.7959 EGB = -7967.1170 1-4 VDW = 1784.2710 1-4 EEL = 23367.0904 RESTRAINT = 0.0000 ESURF = 188.5631 minimization completed, ENE= -.10778862E+05 RMS= 0.172144E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0665E+04 1.7226E+01 1.2720E+02 PB 7842 BOND = 1421.5968 ANGLE = 3739.0151 DIHED = 5401.5324 VDWAALS = -3826.8778 EEL = -34771.5172 EGB = -7953.3644 1-4 VDW = 1813.3389 1-4 EEL = 23322.0345 RESTRAINT = 0.0000 ESURF = 189.3560 minimization completed, ENE= -.10664886E+05 RMS= 0.172258E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0594E+04 1.7510E+01 1.2152E+02 CA 1953 BOND = 1434.9414 ANGLE = 3787.0152 DIHED = 5379.7212 VDWAALS = -3868.6219 EEL = -34808.1362 EGB = -7937.9210 1-4 VDW = 1812.1106 1-4 EEL = 23418.1694 RESTRAINT = 0.0000 ESURF = 188.9012 minimization completed, ENE= -.10593820E+05 RMS= 0.175096E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0594E+04 1.7599E+01 1.1758E+02 C 3459 BOND = 1401.8509 ANGLE = 3765.6280 DIHED = 5442.4129 VDWAALS = -3888.8723 EEL = -34709.6287 EGB = -7991.7542 1-4 VDW = 1809.0370 1-4 EEL = 23388.9311 RESTRAINT = 0.0000 ESURF = 188.6446 minimization completed, ENE= -.10593751E+05 RMS= 0.175994E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0731E+04 1.7250E+01 1.1803E+02 CG 7309 BOND = 1405.6365 ANGLE = 3677.0809 DIHED = 5373.4549 VDWAALS = -3893.8378 EEL = -34845.9852 EGB = -7803.5059 1-4 VDW = 1812.7562 1-4 EEL = 23356.0847 RESTRAINT = 0.0000 ESURF = 187.8124 minimization completed, ENE= -.10730503E+05 RMS= 0.172500E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0577E+04 1.7531E+01 1.3295E+02 CG 598 BOND = 1438.5909 ANGLE = 3800.6271 DIHED = 5414.8284 VDWAALS = -3856.1213 EEL = -34908.5330 EGB = -7858.0969 1-4 VDW = 1830.7725 1-4 EEL = 23372.2388 RESTRAINT = 0.0000 ESURF = 189.1688 minimization completed, ENE= -.10576525E+05 RMS= 0.175306E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0710E+04 1.7570E+01 1.2108E+02 C 2368 BOND = 1477.1526 ANGLE = 3712.1865 DIHED = 5411.6091 VDWAALS = -3886.1486 EEL = -34713.3066 EGB = -7954.1496 1-4 VDW = 1791.1175 1-4 EEL = 23262.6026 RESTRAINT = 0.0000 ESURF = 189.1882 minimization completed, ENE= -.10709748E+05 RMS= 0.175702E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0625E+04 1.7458E+01 1.2906E+02 N 6622 BOND = 1444.4211 ANGLE = 3771.2399 DIHED = 5441.6553 VDWAALS = -3852.9634 EEL = -34822.5097 EGB = -7924.1536 1-4 VDW = 1785.6952 1-4 EEL = 23342.2879 RESTRAINT = 0.0000 ESURF = 189.5432 minimization completed, ENE= -.10624784E+05 RMS= 0.174580E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0730E+04 1.7372E+01 1.1984E+02 C 4154 BOND = 1430.8187 ANGLE = 3703.3083 DIHED = 5381.2878 VDWAALS = -3858.9653 EEL = -34757.3720 EGB = -7950.2775 1-4 VDW = 1796.5981 1-4 EEL = 23336.5556 RESTRAINT = 0.0000 ESURF = 188.5006 minimization completed, ENE= -.10729546E+05 RMS= 0.173716E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0689E+04 1.7345E+01 1.1861E+02 C 2086 BOND = 1430.2927 ANGLE = 3769.0800 DIHED = 5403.1814 VDWAALS = -3884.0419 EEL = -34632.3702 EGB = -8053.6881 1-4 VDW = 1801.9212 1-4 EEL = 23288.7550 RESTRAINT = 0.0000 ESURF = 187.7548 minimization completed, ENE= -.10689115E+05 RMS= 0.173451E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0759E+04 1.7056E+01 1.2077E+02 C 1586 BOND = 1378.9535 ANGLE = 3677.0845 DIHED = 5405.9477 VDWAALS = -3871.2317 EEL = -34791.1129 EGB = -7955.4667 1-4 VDW = 1812.6302 1-4 EEL = 23396.7065 RESTRAINT = 0.0000 ESURF = 187.9771 minimization completed, ENE= -.10758512E+05 RMS= 0.170556E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0713E+04 1.7321E+01 1.3410E+02 CZ 7483 BOND = 1383.3919 ANGLE = 3765.5073 DIHED = 5399.2489 VDWAALS = -3889.1312 EEL = -34785.0455 EGB = -7942.3837 1-4 VDW = 1794.8155 1-4 EEL = 23372.9264 RESTRAINT = 0.0000 ESURF = 187.8760 minimization completed, ENE= -.10712794E+05 RMS= 0.173213E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0639E+04 1.7361E+01 1.0820E+02 C 4465 BOND = 1461.6334 ANGLE = 3779.2736 DIHED = 5466.6841 VDWAALS = -3896.8460 EEL = -35061.4189 EGB = -7658.3808 1-4 VDW = 1771.1191 1-4 EEL = 23312.0188 RESTRAINT = 0.0000 ESURF = 187.0034 minimization completed, ENE= -.10638913E+05 RMS= 0.173609E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 717.10 ( 7.96% of Gen B) | Calc gb diag 5287.58 (58.71% of Gen B) | Calc gb off-diag 3001.67 (33.33% of Gen B) | Gen Born time 9006.35 (100.0% of Nonbo) | Nonbond force 9006.35 (100.0% of Force) | Bond/Angle/Dihedral 8.86 ( 0.10% of Force) | Force time 9015.22 (100.0% of Runmd) | Runmd Time 9015.22 (99.04% of Total) | Other 87.34 ( 0.96% of Total) | Total time 9102.58 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 00:30:19.053 on 10/20/2010 | Setup done at 00:30:20.288 on 10/20/2010 | Run done at 03:02:01.630 on 10/20/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/20/2010 at 00:30:19 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _lig.out.15 |INPCRD: 1XCK_chainA_MGATP_noWAT.inpcrd | PARM: 1XCK_chainA_MGATP_noWAT.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _lig.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 = 09/24/09 Time = 02:43:23 NATOM = 7879 NTYPES = 18 NBONH = 3991 MBONA = 3917 NTHETH = 9115 MTHETA = 5297 NPHIH = 17023 MPHIA = 12427 NHPARM = 0 NPARM = 0 NNB = 43422 NRES = 526 NBONA = 3917 NTHETA = 5297 NPHIA = 12427 NUMBND = 52 NUMANG = 108 NPTRA = 66 NATYP = 36 NPHB = 0 IFBOX = 0 NMXRS = 43 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 567848 | Hollerith 24165 | Integer 1061772 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 8678 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 -1.0782E+04 1.7286E+01 1.1359E+02 CA 1963 BOND = 1393.6733 ANGLE = 3680.9376 DIHED = 5404.4632 VDWAALS = -3911.1650 EEL = -34957.9702 EGB = -7634.1522 1-4 VDW = 1810.1236 1-4 EEL = 23247.6030 RESTRAINT = 0.0000 ESURF = 184.1134 minimization completed, ENE= -.10782373E+05 RMS= 0.172858E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0683E+04 1.7420E+01 1.2173E+02 C 5983 BOND = 1396.7895 ANGLE = 3764.4560 DIHED = 5417.8444 VDWAALS = -3896.1640 EEL = -35033.0682 EGB = -7720.1213 1-4 VDW = 1811.1989 1-4 EEL = 23387.4588 RESTRAINT = 0.0000 ESURF = 188.1384 minimization completed, ENE= -.10683467E+05 RMS= 0.174196E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0753E+04 1.7472E+01 1.0355E+02 C 1035 BOND = 1403.0929 ANGLE = 3745.1178 DIHED = 5402.8729 VDWAALS = -3868.0210 EEL = -34977.1426 EGB = -7727.4860 1-4 VDW = 1804.5462 1-4 EEL = 23276.3134 RESTRAINT = 0.0000 ESURF = 187.7981 minimization completed, ENE= -.10752908E+05 RMS= 0.174720E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0793E+04 1.7296E+01 1.1980E+02 CD 2701 BOND = 1441.3010 ANGLE = 3657.9787 DIHED = 5429.4933 VDWAALS = -3900.5109 EEL = -35091.5203 EGB = -7664.3248 1-4 VDW = 1803.9252 1-4 EEL = 23345.3270 RESTRAINT = 0.0000 ESURF = 184.8751 minimization completed, ENE= -.10793456E+05 RMS= 0.172958E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0743E+04 1.7355E+01 1.1182E+02 CA 5960 BOND = 1426.2701 ANGLE = 3748.6910 DIHED = 5412.3859 VDWAALS = -3894.6706 EEL = -35108.9707 EGB = -7622.2472 1-4 VDW = 1787.5132 1-4 EEL = 23320.6854 RESTRAINT = 0.0000 ESURF = 186.9223 minimization completed, ENE= -.10743421E+05 RMS= 0.173547E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0631E+04 1.7539E+01 1.1792E+02 CG 4904 BOND = 1472.8322 ANGLE = 3802.2406 DIHED = 5387.5497 VDWAALS = -3872.9684 EEL = -35066.3016 EGB = -7681.2027 1-4 VDW = 1816.3381 1-4 EEL = 23325.3441 RESTRAINT = 0.0000 ESURF = 185.5656 minimization completed, ENE= -.10630602E+05 RMS= 0.175394E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0706E+04 1.7556E+01 1.1915E+02 C 2586 BOND = 1420.8054 ANGLE = 3768.7958 DIHED = 5384.9017 VDWAALS = -3910.3618 EEL = -34902.3029 EGB = -7789.7146 1-4 VDW = 1801.0520 1-4 EEL = 23335.0860 RESTRAINT = 0.0000 ESURF = 185.3494 minimization completed, ENE= -.10706389E+05 RMS= 0.175559E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0708E+04 1.7616E+01 1.2147E+02 C 5029 BOND = 1464.7828 ANGLE = 3685.0111 DIHED = 5407.6254 VDWAALS = -3848.8621 EEL = -34843.8365 EGB = -7936.9668 1-4 VDW = 1805.3525 1-4 EEL = 23372.7179 RESTRAINT = 0.0000 ESURF = 186.2956 minimization completed, ENE= -.10707880E+05 RMS= 0.176158E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0760E+04 1.7164E+01 1.1367E+02 C 2751 BOND = 1367.7302 ANGLE = 3737.0158 DIHED = 5405.9138 VDWAALS = -3882.6730 EEL = -34836.5562 EGB = -7911.7404 1-4 VDW = 1816.9267 1-4 EEL = 23355.8073 RESTRAINT = 0.0000 ESURF = 187.5579 minimization completed, ENE= -.10760018E+05 RMS= 0.171645E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0607E+04 1.7671E+01 1.1053E+02 C 6956 BOND = 1474.7938 ANGLE = 3798.6747 DIHED = 5443.7829 VDWAALS = -3893.6453 EEL = -34843.1059 EGB = -7808.7480 1-4 VDW = 1794.2962 1-4 EEL = 23239.7363 RESTRAINT = 0.0000 ESURF = 187.3496 minimization completed, ENE= -.10606866E+05 RMS= 0.176713E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0736E+04 1.7444E+01 1.1877E+02 CZ 7483 BOND = 1438.4475 ANGLE = 3710.9514 DIHED = 5389.9487 VDWAALS = -3838.1224 EEL = -34893.7442 EGB = -7876.2437 1-4 VDW = 1809.8540 1-4 EEL = 23335.1645 RESTRAINT = 0.0000 ESURF = 187.3225 minimization completed, ENE= -.10736422E+05 RMS= 0.174437E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0692E+04 1.7394E+01 1.1492E+02 C 5971 BOND = 1445.4637 ANGLE = 3758.3297 DIHED = 5379.5145 VDWAALS = -3934.1686 EEL = -34740.4554 EGB = -7923.7644 1-4 VDW = 1807.0292 1-4 EEL = 23328.5363 RESTRAINT = 0.0000 ESURF = 187.5536 minimization completed, ENE= -.10691961E+05 RMS= 0.173939E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0709E+04 1.7404E+01 1.0827E+02 C 5006 BOND = 1429.1286 ANGLE = 3752.4572 DIHED = 5396.9913 VDWAALS = -3896.1275 EEL = -34891.2977 EGB = -7834.2251 1-4 VDW = 1790.0538 1-4 EEL = 23354.4675 RESTRAINT = 0.0000 ESURF = 189.4557 minimization completed, ENE= -.10709096E+05 RMS= 0.174045E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0711E+04 1.7239E+01 1.1004E+02 CD 2672 BOND = 1398.6722 ANGLE = 3767.3983 DIHED = 5378.4048 VDWAALS = -3860.4919 EEL = -34987.9648 EGB = -7825.6966 1-4 VDW = 1833.1249 1-4 EEL = 23398.3543 RESTRAINT = 0.0000 ESURF = 186.9079 minimization completed, ENE= -.10711291E+05 RMS= 0.172389E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0635E+04 1.7556E+01 1.2177E+02 C 1156 BOND = 1480.2336 ANGLE = 3737.0130 DIHED = 5451.4815 VDWAALS = -3868.8205 EEL = -34974.7304 EGB = -7840.1305 1-4 VDW = 1789.0422 1-4 EEL = 23403.6878 RESTRAINT = 0.0000 ESURF = 187.2738 minimization completed, ENE= -.10634949E+05 RMS= 0.175561E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0687E+04 1.7348E+01 1.1055E+02 CG1 2191 BOND = 1392.7749 ANGLE = 3815.4883 DIHED = 5417.3939 VDWAALS = -3939.4090 EEL = -34715.6540 EGB = -8027.2113 1-4 VDW = 1796.7806 1-4 EEL = 23385.4689 RESTRAINT = 0.0000 ESURF = 187.5041 minimization completed, ENE= -.10686864E+05 RMS= 0.173478E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0742E+04 1.7355E+01 1.0618E+02 C 1325 BOND = 1436.1006 ANGLE = 3681.1306 DIHED = 5386.5939 VDWAALS = -3881.6413 EEL = -34901.0526 EGB = -7824.5318 1-4 VDW = 1809.8151 1-4 EEL = 23364.6909 RESTRAINT = 0.0000 ESURF = 186.4051 minimization completed, ENE= -.10742489E+05 RMS= 0.173554E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0765E+04 1.7362E+01 1.1014E+02 CD 5056 BOND = 1449.3843 ANGLE = 3693.5037 DIHED = 5398.0028 VDWAALS = -3861.0051 EEL = -35025.7106 EGB = -7751.3054 1-4 VDW = 1798.1291 1-4 EEL = 23347.0574 RESTRAINT = 0.0000 ESURF = 187.2577 minimization completed, ENE= -.10764686E+05 RMS= 0.173623E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0626E+04 1.7484E+01 1.1972E+02 C 6468 BOND = 1427.3626 ANGLE = 3742.0253 DIHED = 5413.9962 VDWAALS = -3810.7639 EEL = -34921.0286 EGB = -7809.2904 1-4 VDW = 1826.6740 1-4 EEL = 23315.4139 RESTRAINT = 0.0000 ESURF = 189.7852 minimization completed, ENE= -.10625826E+05 RMS= 0.174840E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0730E+04 1.7488E+01 1.0630E+02 C 2556 BOND = 1421.9203 ANGLE = 3700.4347 DIHED = 5414.3448 VDWAALS = -3828.8712 EEL = -34733.0833 EGB = -8076.6407 1-4 VDW = 1819.8258 1-4 EEL = 23361.4077 RESTRAINT = 0.0000 ESURF = 190.6266 minimization completed, ENE= -.10730035E+05 RMS= 0.174880E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0730E+04 1.7175E+01 1.1352E+02 N 6542 BOND = 1375.0260 ANGLE = 3763.9770 DIHED = 5411.7602 VDWAALS = -3877.7820 EEL = -34746.7297 EGB = -7952.9112 1-4 VDW = 1812.5580 1-4 EEL = 23294.6641 RESTRAINT = 0.0000 ESURF = 189.0586 minimization completed, ENE= -.10730379E+05 RMS= 0.171746E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0746E+04 1.7334E+01 1.1397E+02 N 3806 BOND = 1399.4748 ANGLE = 3752.4889 DIHED = 5415.7530 VDWAALS = -3887.3146 EEL = -34751.6619 EGB = -8043.3457 1-4 VDW = 1798.2457 1-4 EEL = 23379.6910 RESTRAINT = 0.0000 ESURF = 190.7339 minimization completed, ENE= -.10745935E+05 RMS= 0.173338E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0763E+04 1.7272E+01 1.1634E+02 C 7250 BOND = 1422.5209 ANGLE = 3688.6378 DIHED = 5457.5273 VDWAALS = -3899.1966 EEL = -34603.3174 EGB = -8114.3235 1-4 VDW = 1783.2224 1-4 EEL = 23311.4267 RESTRAINT = 0.0000 ESURF = 190.6268 minimization completed, ENE= -.10762875E+05 RMS= 0.172722E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0686E+04 1.7271E+01 1.2378E+02 C 5762 BOND = 1464.5957 ANGLE = 3752.2796 DIHED = 5403.8125 VDWAALS = -3897.0972 EEL = -34703.4569 EGB = -7981.5390 1-4 VDW = 1785.7630 1-4 EEL = 23301.7435 RESTRAINT = 0.0000 ESURF = 188.0552 minimization completed, ENE= -.10685843E+05 RMS= 0.172709E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0751E+04 1.7356E+01 1.1917E+02 CD 2598 BOND = 1450.0953 ANGLE = 3727.2161 DIHED = 5359.5793 VDWAALS = -3886.3170 EEL = -34894.1974 EGB = -7821.3598 1-4 VDW = 1796.1591 1-4 EEL = 23329.3056 RESTRAINT = 0.0000 ESURF = 188.4081 minimization completed, ENE= -.10751111E+05 RMS= 0.173562E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0799E+04 1.7269E+01 1.3855E+02 C 3172 BOND = 1420.3701 ANGLE = 3743.8527 DIHED = 5376.7420 VDWAALS = -3868.8982 EEL = -34831.7050 EGB = -7977.3266 1-4 VDW = 1776.9326 1-4 EEL = 23369.1635 RESTRAINT = 0.0000 ESURF = 191.9249 minimization completed, ENE= -.10798944E+05 RMS= 0.172692E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0781E+04 1.7503E+01 1.2823E+02 C 3047 BOND = 1458.2647 ANGLE = 3702.1082 DIHED = 5389.4967 VDWAALS = -3839.7435 EEL = -34924.1591 EGB = -7883.9739 1-4 VDW = 1766.8419 1-4 EEL = 23359.4253 RESTRAINT = 0.0000 ESURF = 191.0762 minimization completed, ENE= -.10780664E+05 RMS= 0.175027E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0736E+04 1.7370E+01 1.1253E+02 C 2907 BOND = 1432.3070 ANGLE = 3717.4980 DIHED = 5387.0824 VDWAALS = -3891.0904 EEL = -34795.5053 EGB = -7927.0372 1-4 VDW = 1802.5674 1-4 EEL = 23347.4722 RESTRAINT = 0.0000 ESURF = 190.4867 minimization completed, ENE= -.10736219E+05 RMS= 0.173696E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0643E+04 1.7386E+01 1.3037E+02 CB 4955 BOND = 1373.9868 ANGLE = 3771.4529 DIHED = 5409.7535 VDWAALS = -3864.2039 EEL = -34925.3450 EGB = -7913.0593 1-4 VDW = 1853.2074 1-4 EEL = 23459.9787 RESTRAINT = 0.0000 ESURF = 191.3899 minimization completed, ENE= -.10642839E+05 RMS= 0.173862E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0837E+04 1.7385E+01 1.0788E+02 CB 1331 BOND = 1386.0491 ANGLE = 3710.3521 DIHED = 5416.3900 VDWAALS = -3894.6693 EEL = -34900.4831 EGB = -7922.4208 1-4 VDW = 1792.4278 1-4 EEL = 23384.1058 RESTRAINT = 0.0000 ESURF = 190.9669 minimization completed, ENE= -.10837281E+05 RMS= 0.173852E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0657E+04 1.7310E+01 1.1876E+02 CD 5774 BOND = 1408.9241 ANGLE = 3801.4489 DIHED = 5392.8374 VDWAALS = -3871.2283 EEL = -34750.3471 EGB = -7990.2791 1-4 VDW = 1813.7796 1-4 EEL = 23347.6549 RESTRAINT = 0.0000 ESURF = 190.4014 minimization completed, ENE= -.10656808E+05 RMS= 0.173101E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0681E+04 1.7554E+01 1.1706E+02 CD 2779 BOND = 1466.6814 ANGLE = 3761.1030 DIHED = 5385.5644 VDWAALS = -3896.2019 EEL = -34677.9850 EGB = -8039.1381 1-4 VDW = 1756.5094 1-4 EEL = 23372.0284 RESTRAINT = 0.0000 ESURF = 190.1640 minimization completed, ENE= -.10681274E+05 RMS= 0.175538E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0740E+04 1.7303E+01 1.1290E+02 C 1893 BOND = 1399.8458 ANGLE = 3729.8806 DIHED = 5404.7721 VDWAALS = -3851.3118 EEL = -34825.9623 EGB = -7992.8491 1-4 VDW = 1816.5547 1-4 EEL = 23386.5019 RESTRAINT = 0.0000 ESURF = 192.8108 minimization completed, ENE= -.10739757E+05 RMS= 0.173032E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0686E+04 1.7119E+01 1.1458E+02 N 1121 BOND = 1399.6882 ANGLE = 3778.3192 DIHED = 5373.2207 VDWAALS = -3857.7921 EEL = -34916.1348 EGB = -7866.1343 1-4 VDW = 1800.5044 1-4 EEL = 23413.6489 RESTRAINT = 0.0000 ESURF = 189.1461 minimization completed, ENE= -.10685534E+05 RMS= 0.171195E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0725E+04 1.7126E+01 1.0102E+02 CA 1123 BOND = 1350.7449 ANGLE = 3789.5599 DIHED = 5369.4870 VDWAALS = -3851.9103 EEL = -34994.2828 EGB = -7783.2172 1-4 VDW = 1822.7433 1-4 EEL = 23380.8611 RESTRAINT = 0.0000 ESURF = 191.4560 minimization completed, ENE= -.10724558E+05 RMS= 0.171264E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0544E+04 1.7575E+01 1.1835E+02 CG 3379 BOND = 1456.1528 ANGLE = 3878.1988 DIHED = 5426.3671 VDWAALS = -3870.7963 EEL = -34851.7082 EGB = -7895.4451 1-4 VDW = 1801.1900 1-4 EEL = 23324.6875 RESTRAINT = 0.0000 ESURF = 187.7781 minimization completed, ENE= -.10543575E+05 RMS= 0.175751E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0687E+04 1.7372E+01 1.1425E+02 C 7501 BOND = 1417.4471 ANGLE = 3698.7918 DIHED = 5418.7255 VDWAALS = -3827.0193 EEL = -34798.0392 EGB = -7884.2273 1-4 VDW = 1817.7570 1-4 EEL = 23281.0199 RESTRAINT = 0.0000 ESURF = 188.7900 minimization completed, ENE= -.10686755E+05 RMS= 0.173719E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0774E+04 1.7276E+01 1.1409E+02 CD 6897 BOND = 1426.4961 ANGLE = 3701.2006 DIHED = 5409.1663 VDWAALS = -3887.2092 EEL = -34939.0772 EGB = -7822.7824 1-4 VDW = 1799.6166 1-4 EEL = 23351.1538 RESTRAINT = 0.0000 ESURF = 187.4667 minimization completed, ENE= -.10773969E+05 RMS= 0.172758E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0696E+04 1.7232E+01 1.0769E+02 C 7741 BOND = 1443.6583 ANGLE = 3711.8791 DIHED = 5395.1462 VDWAALS = -3868.6571 EEL = -34873.4657 EGB = -7803.1381 1-4 VDW = 1787.2700 1-4 EEL = 23323.5072 RESTRAINT = 0.0000 ESURF = 187.7677 minimization completed, ENE= -.10696033E+05 RMS= 0.172316E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0733E+04 1.7355E+01 1.2202E+02 C 2937 BOND = 1373.8977 ANGLE = 3704.0975 DIHED = 5389.3444 VDWAALS = -3871.7932 EEL = -34964.8044 EGB = -7738.1585 1-4 VDW = 1842.7049 1-4 EEL = 23345.4183 RESTRAINT = 0.0000 ESURF = 186.0005 minimization completed, ENE= -.10733293E+05 RMS= 0.173554E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0688E+04 1.7297E+01 1.1230E+02 CG 7309 BOND = 1458.0179 ANGLE = 3665.9187 DIHED = 5443.8379 VDWAALS = -3862.5269 EEL = -34793.0030 EGB = -7878.6216 1-4 VDW = 1792.0699 1-4 EEL = 23298.2502 RESTRAINT = 0.0000 ESURF = 188.2606 minimization completed, ENE= -.10687796E+05 RMS= 0.172975E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0771E+04 1.7231E+01 1.1866E+02 N 5864 BOND = 1422.0840 ANGLE = 3645.5917 DIHED = 5430.0716 VDWAALS = -3857.9284 EEL = -34891.2676 EGB = -7885.8047 1-4 VDW = 1803.2346 1-4 EEL = 23374.5667 RESTRAINT = 0.0000 ESURF = 188.6790 minimization completed, ENE= -.10770773E+05 RMS= 0.172310E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0791E+04 1.7313E+01 1.0388E+02 C 6582 BOND = 1368.8441 ANGLE = 3735.9425 DIHED = 5416.8969 VDWAALS = -3895.6631 EEL = -34700.9159 EGB = -7997.4535 1-4 VDW = 1785.7392 1-4 EEL = 23307.9121 RESTRAINT = 0.0000 ESURF = 187.7881 minimization completed, ENE= -.10790910E+05 RMS= 0.173129E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0792E+04 1.7199E+01 1.1443E+02 C 2907 BOND = 1388.0194 ANGLE = 3681.3169 DIHED = 5412.0108 VDWAALS = -3898.0573 EEL = -34757.3083 EGB = -7936.3789 1-4 VDW = 1787.4473 1-4 EEL = 23344.1082 RESTRAINT = 0.0000 ESURF = 186.8451 minimization completed, ENE= -.10791997E+05 RMS= 0.171989E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0756E+04 1.7528E+01 9.6756E+01 C 1059 BOND = 1408.1304 ANGLE = 3666.0897 DIHED = 5374.9527 VDWAALS = -3908.4994 EEL = -34619.2761 EGB = -8004.6483 1-4 VDW = 1815.9827 1-4 EEL = 23323.9018 RESTRAINT = 0.0000 ESURF = 187.2016 minimization completed, ENE= -.10756165E+05 RMS= 0.175277E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0717E+04 1.7286E+01 9.9146E+01 C 5916 BOND = 1386.7502 ANGLE = 3772.2185 DIHED = 5382.8208 VDWAALS = -3842.1966 EEL = -34914.1427 EGB = -7870.3701 1-4 VDW = 1817.3992 1-4 EEL = 23361.6689 RESTRAINT = 0.0000 ESURF = 188.5899 minimization completed, ENE= -.10717262E+05 RMS= 0.172860E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0776E+04 1.7357E+01 1.2987E+02 CD 2511 BOND = 1440.0267 ANGLE = 3744.5052 DIHED = 5387.0992 VDWAALS = -3878.5012 EEL = -35064.9088 EGB = -7686.7633 1-4 VDW = 1768.3123 1-4 EEL = 23325.9405 RESTRAINT = 0.0000 ESURF = 188.0947 minimization completed, ENE= -.10776195E+05 RMS= 0.173567E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0629E+04 1.7330E+01 1.0302E+02 CD 6521 BOND = 1435.0533 ANGLE = 3746.2241 DIHED = 5454.9701 VDWAALS = -3838.7971 EEL = -34884.2964 EGB = -7914.6353 1-4 VDW = 1788.0632 1-4 EEL = 23394.6093 RESTRAINT = 0.0000 ESURF = 190.2084 minimization completed, ENE= -.10628601E+05 RMS= 0.173304E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0720E+04 1.7218E+01 1.1910E+02 CG 4342 BOND = 1408.6022 ANGLE = 3789.2700 DIHED = 5402.6894 VDWAALS = -3932.0161 EEL = -34708.4270 EGB = -8036.0489 1-4 VDW = 1785.2544 1-4 EEL = 23381.8840 RESTRAINT = 0.0000 ESURF = 188.4493 minimization completed, ENE= -.10720343E+05 RMS= 0.172179E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0781E+04 1.7028E+01 1.0816E+02 N 6391 BOND = 1345.6565 ANGLE = 3775.2044 DIHED = 5370.5886 VDWAALS = -3845.4680 EEL = -34773.1702 EGB = -8058.1918 1-4 VDW = 1811.3441 1-4 EEL = 23405.1674 RESTRAINT = 0.0000 ESURF = 187.9347 minimization completed, ENE= -.10780934E+05 RMS= 0.170282E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 677.02 ( 7.54% of Gen B) | Calc gb diag 5332.33 (59.42% of Gen B) | Calc gb off-diag 2963.92 (33.03% of Gen B) | Gen Born time 8973.27 (100.0% of Nonbo) | Nonbond force 8973.27 (99.89% of Force) | Bond/Angle/Dihedral 9.72 ( 0.11% of Force) | Force time 8983.00 (100.0% of Runmd) | Runmd Time 8983.00 (98.97% of Total) | Other 93.52 ( 1.03% of Total) | Total time 9076.54 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 00:30:16.963 on 10/20/2010 | Setup done at 00:30:21.906 on 10/20/2010 | Run done at 03:01:33.507 on 10/20/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/20/2010 at 00:30:21 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _lig.out.14 |INPCRD: 1XCK_chainA_MGATP_noWAT.inpcrd | PARM: 1XCK_chainA_MGATP_noWAT.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _lig.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 = 09/24/09 Time = 02:43:23 NATOM = 7879 NTYPES = 18 NBONH = 3991 MBONA = 3917 NTHETH = 9115 MTHETA = 5297 NPHIH = 17023 MPHIA = 12427 NHPARM = 0 NPARM = 0 NNB = 43422 NRES = 526 NBONA = 3917 NTHETA = 5297 NPHIA = 12427 NUMBND = 52 NUMANG = 108 NPTRA = 66 NATYP = 36 NPHB = 0 IFBOX = 0 NMXRS = 43 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 567848 | Hollerith 24165 | Integer 1061772 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 8678 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 -1.0664E+04 1.7349E+01 1.1435E+02 CG 782 BOND = 1468.6353 ANGLE = 3726.3575 DIHED = 5418.9912 VDWAALS = -3868.5073 EEL = -34668.2231 EGB = -8030.7009 1-4 VDW = 1805.3482 1-4 EEL = 23296.0390 RESTRAINT = 0.0000 ESURF = 188.4919 minimization completed, ENE= -.10663568E+05 RMS= 0.173491E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0778E+04 1.7475E+01 1.2501E+02 C 235 BOND = 1448.3250 ANGLE = 3675.6207 DIHED = 5422.7259 VDWAALS = -3884.9238 EEL = -34657.9041 EGB = -8082.0203 1-4 VDW = 1765.0864 1-4 EEL = 23346.3368 RESTRAINT = 0.0000 ESURF = 188.2911 minimization completed, ENE= -.10778462E+05 RMS= 0.174747E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0743E+04 1.7069E+01 1.2332E+02 CA 7636 BOND = 1385.8645 ANGLE = 3688.1884 DIHED = 5423.7921 VDWAALS = -3861.0458 EEL = -34678.4439 EGB = -8045.3306 1-4 VDW = 1810.6247 1-4 EEL = 23346.3965 RESTRAINT = 0.0000 ESURF = 187.3151 minimization completed, ENE= -.10742639E+05 RMS= 0.170689E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0760E+04 1.7260E+01 1.1923E+02 C 5098 BOND = 1405.3393 ANGLE = 3743.5060 DIHED = 5413.0788 VDWAALS = -3924.7000 EEL = -34584.7663 EGB = -8042.3654 1-4 VDW = 1806.5668 1-4 EEL = 23236.2170 RESTRAINT = 0.0000 ESURF = 187.4486 minimization completed, ENE= -.10759675E+05 RMS= 0.172601E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0697E+04 1.7342E+01 1.2281E+02 C 7715 BOND = 1379.3321 ANGLE = 3684.2873 DIHED = 5465.5590 VDWAALS = -3867.1559 EEL = -34757.0712 EGB = -7968.0704 1-4 VDW = 1833.4647 1-4 EEL = 23344.5161 RESTRAINT = 0.0000 ESURF = 187.9584 minimization completed, ENE= -.10697180E+05 RMS= 0.173415E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0760E+04 1.7380E+01 1.2164E+02 C 7074 BOND = 1440.5767 ANGLE = 3645.2358 DIHED = 5420.5213 VDWAALS = -3850.7629 EEL = -34718.2285 EGB = -7951.9852 1-4 VDW = 1787.0512 1-4 EEL = 23279.3283 RESTRAINT = 0.0000 ESURF = 188.0394 minimization completed, ENE= -.10760224E+05 RMS= 0.173799E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0737E+04 1.7297E+01 1.1941E+02 C 4663 BOND = 1411.3065 ANGLE = 3706.4084 DIHED = 5423.6685 VDWAALS = -3915.1607 EEL = -34820.6628 EGB = -7933.3287 1-4 VDW = 1802.3081 1-4 EEL = 23401.8490 RESTRAINT = 0.0000 ESURF = 186.4295 minimization completed, ENE= -.10737182E+05 RMS= 0.172965E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0734E+04 1.7568E+01 1.2572E+02 C 6834 BOND = 1443.9317 ANGLE = 3682.6674 DIHED = 5411.3454 VDWAALS = -3850.5348 EEL = -34886.6282 EGB = -7945.2228 1-4 VDW = 1808.1551 1-4 EEL = 23414.9632 RESTRAINT = 0.0000 ESURF = 187.0221 minimization completed, ENE= -.10734301E+05 RMS= 0.175675E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0655E+04 1.7395E+01 1.1403E+02 C 7074 BOND = 1419.3199 ANGLE = 3726.4262 DIHED = 5436.8798 VDWAALS = -3877.2937 EEL = -34610.7012 EGB = -8061.7320 1-4 VDW = 1830.5163 1-4 EEL = 23292.7694 RESTRAINT = 0.0000 ESURF = 188.8969 minimization completed, ENE= -.10654919E+05 RMS= 0.173950E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0706E+04 1.7503E+01 1.2282E+02 N 7302 BOND = 1422.3438 ANGLE = 3698.4734 DIHED = 5401.8705 VDWAALS = -3883.9257 EEL = -34629.7790 EGB = -8103.7259 1-4 VDW = 1809.9789 1-4 EEL = 23389.9615 RESTRAINT = 0.0000 ESURF = 188.4644 minimization completed, ENE= -.10706338E+05 RMS= 0.175027E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0703E+04 1.7323E+01 1.1152E+02 CD 4507 BOND = 1443.6409 ANGLE = 3714.6463 DIHED = 5432.6012 VDWAALS = -3898.1043 EEL = -34757.4110 EGB = -8012.8571 1-4 VDW = 1842.1112 1-4 EEL = 23347.7605 RESTRAINT = 0.0000 ESURF = 184.8227 minimization completed, ENE= -.10702790E+05 RMS= 0.173232E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0616E+04 1.7314E+01 1.1532E+02 C 43 BOND = 1408.8746 ANGLE = 3822.1851 DIHED = 5409.3904 VDWAALS = -3864.2454 EEL = -34683.5808 EGB = -7956.4808 1-4 VDW = 1791.5666 1-4 EEL = 23269.3113 RESTRAINT = 0.0000 ESURF = 186.5915 minimization completed, ENE= -.10616388E+05 RMS= 0.173137E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0686E+04 1.7424E+01 1.1404E+02 C 1311 BOND = 1428.8168 ANGLE = 3764.0203 DIHED = 5411.0368 VDWAALS = -3899.7406 EEL = -34868.7706 EGB = -7789.9715 1-4 VDW = 1810.0132 1-4 EEL = 23272.5084 RESTRAINT = 0.0000 ESURF = 185.9151 minimization completed, ENE= -.10686172E+05 RMS= 0.174237E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0641E+04 1.7335E+01 1.0890E+02 C 3508 BOND = 1393.9336 ANGLE = 3795.9371 DIHED = 5394.6016 VDWAALS = -3897.2404 EEL = -34779.9519 EGB = -7787.6104 1-4 VDW = 1799.7108 1-4 EEL = 23254.6354 RESTRAINT = 0.0000 ESURF = 185.1210 minimization completed, ENE= -.10640863E+05 RMS= 0.173346E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0708E+04 1.7418E+01 1.1715E+02 C 2368 BOND = 1429.1600 ANGLE = 3739.6331 DIHED = 5377.0354 VDWAALS = -3859.7117 EEL = -34891.8716 EGB = -7780.2933 1-4 VDW = 1784.9738 1-4 EEL = 23305.0588 RESTRAINT = 0.0000 ESURF = 187.6539 minimization completed, ENE= -.10708362E+05 RMS= 0.174184E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0756E+04 1.7176E+01 1.2493E+02 C 1225 BOND = 1370.4727 ANGLE = 3736.6608 DIHED = 5429.1417 VDWAALS = -3896.6556 EEL = -34919.9327 EGB = -7833.7738 1-4 VDW = 1829.8569 1-4 EEL = 23340.2436 RESTRAINT = 0.0000 ESURF = 187.9252 minimization completed, ENE= -.10756061E+05 RMS= 0.171762E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0684E+04 1.7367E+01 1.0928E+02 C 4921 BOND = 1417.1688 ANGLE = 3712.9884 DIHED = 5407.0543 VDWAALS = -3914.0100 EEL = -34860.5096 EGB = -7826.8862 1-4 VDW = 1819.6044 1-4 EEL = 23374.6799 RESTRAINT = 0.0000 ESURF = 186.3254 minimization completed, ENE= -.10683584E+05 RMS= 0.173672E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0654E+04 1.7380E+01 1.1776E+02 CD 881 BOND = 1453.4741 ANGLE = 3740.2568 DIHED = 5418.1068 VDWAALS = -3900.0003 EEL = -34684.5570 EGB = -7964.5512 1-4 VDW = 1798.7108 1-4 EEL = 23297.4349 RESTRAINT = 0.0000 ESURF = 186.6292 minimization completed, ENE= -.10654496E+05 RMS= 0.173802E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0733E+04 1.7133E+01 1.1285E+02 C 21 BOND = 1399.9839 ANGLE = 3770.2549 DIHED = 5387.2340 VDWAALS = -3871.4859 EEL = -34871.0214 EGB = -7839.0251 1-4 VDW = 1775.7445 1-4 EEL = 23326.4799 RESTRAINT = 0.0000 ESURF = 188.4836 minimization completed, ENE= -.10733352E+05 RMS= 0.171327E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0670E+04 1.7440E+01 1.1868E+02 CG 6862 BOND = 1399.2576 ANGLE = 3780.3412 DIHED = 5429.8480 VDWAALS = -3899.7425 EEL = -34960.2053 EGB = -7723.1627 1-4 VDW = 1782.8393 1-4 EEL = 23332.2603 RESTRAINT = 0.0000 ESURF = 188.8911 minimization completed, ENE= -.10669673E+05 RMS= 0.174398E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0649E+04 1.7342E+01 1.1060E+02 N 7670 BOND = 1416.3838 ANGLE = 3781.7995 DIHED = 5460.2842 VDWAALS = -3867.6578 EEL = -34879.4333 EGB = -7835.9109 1-4 VDW = 1801.1746 1-4 EEL = 23286.8553 RESTRAINT = 0.0000 ESURF = 187.9365 minimization completed, ENE= -.10648568E+05 RMS= 0.173422E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0841E+04 1.7380E+01 1.0687E+02 CZ 4801 BOND = 1452.8706 ANGLE = 3645.8192 DIHED = 5368.6594 VDWAALS = -3878.7276 EEL = -34843.9867 EGB = -7870.9931 1-4 VDW = 1780.6350 1-4 EEL = 23316.4588 RESTRAINT = 0.0000 ESURF = 187.8243 minimization completed, ENE= -.10841440E+05 RMS= 0.173798E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0797E+04 1.6963E+01 1.0905E+02 C 1261 BOND = 1418.0258 ANGLE = 3674.5661 DIHED = 5435.2767 VDWAALS = -3914.3987 EEL = -34759.6517 EGB = -7882.2953 1-4 VDW = 1795.5105 1-4 EEL = 23248.2014 RESTRAINT = 0.0000 ESURF = 188.0473 minimization completed, ENE= -.10796718E+05 RMS= 0.169626E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0720E+04 1.6996E+01 1.0958E+02 ND2 6993 BOND = 1348.4894 ANGLE = 3785.4489 DIHED = 5418.8564 VDWAALS = -3912.3205 EEL = -34790.6252 EGB = -7878.8396 1-4 VDW = 1808.9540 1-4 EEL = 23313.1009 RESTRAINT = 0.0000 ESURF = 186.7408 minimization completed, ENE= -.10720195E+05 RMS= 0.169964E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0767E+04 1.7090E+01 1.0727E+02 C 235 BOND = 1351.0595 ANGLE = 3710.7371 DIHED = 5401.8283 VDWAALS = -3885.8307 EEL = -34824.4958 EGB = -7869.8500 1-4 VDW = 1810.6913 1-4 EEL = 23351.6947 RESTRAINT = 0.0000 ESURF = 186.8470 minimization completed, ENE= -.10767319E+05 RMS= 0.170901E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0659E+04 1.7373E+01 1.0866E+02 C 1103 BOND = 1472.3289 ANGLE = 3697.9459 DIHED = 5446.0567 VDWAALS = -3898.9104 EEL = -34836.7623 EGB = -7882.9719 1-4 VDW = 1805.2931 1-4 EEL = 23352.7707 RESTRAINT = 0.0000 ESURF = 185.7305 minimization completed, ENE= -.10658519E+05 RMS= 0.173729E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0752E+04 1.7068E+01 1.1259E+02 C 3047 BOND = 1378.0945 ANGLE = 3759.4800 DIHED = 5412.1319 VDWAALS = -3824.5339 EEL = -34881.3439 EGB = -7871.4464 1-4 VDW = 1798.1593 1-4 EEL = 23291.1607 RESTRAINT = 0.0000 ESURF = 186.5921 minimization completed, ENE= -.10751706E+05 RMS= 0.170679E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0721E+04 1.7262E+01 1.1227E+02 CD 4507 BOND = 1409.0919 ANGLE = 3711.5653 DIHED = 5457.0586 VDWAALS = -3909.0105 EEL = -34821.8704 EGB = -7934.8062 1-4 VDW = 1795.1420 1-4 EEL = 23386.0530 RESTRAINT = 0.0000 ESURF = 185.4899 minimization completed, ENE= -.10721286E+05 RMS= 0.172622E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0703E+04 1.7473E+01 1.1015E+02 C 1069 BOND = 1428.4506 ANGLE = 3782.9010 DIHED = 5386.3008 VDWAALS = -3882.9215 EEL = -34778.6026 EGB = -7949.3899 1-4 VDW = 1808.2282 1-4 EEL = 23315.0576 RESTRAINT = 0.0000 ESURF = 186.5244 minimization completed, ENE= -.10703451E+05 RMS= 0.174735E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0665E+04 1.7178E+01 1.2900E+02 C 5395 BOND = 1374.5143 ANGLE = 3748.0262 DIHED = 5427.2667 VDWAALS = -3860.3221 EEL = -34847.4580 EGB = -7807.9028 1-4 VDW = 1810.7160 1-4 EEL = 23302.9861 RESTRAINT = 0.0000 ESURF = 187.5985 minimization completed, ENE= -.10664575E+05 RMS= 0.171779E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0738E+04 1.7055E+01 1.1209E+02 CD 4694 BOND = 1357.9350 ANGLE = 3788.7141 DIHED = 5397.3655 VDWAALS = -3904.2067 EEL = -34739.7299 EGB = -7975.6329 1-4 VDW = 1799.5632 1-4 EEL = 23351.3108 RESTRAINT = 0.0000 ESURF = 187.0990 minimization completed, ENE= -.10737582E+05 RMS= 0.170551E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0779E+04 1.7107E+01 1.0735E+02 CZ 862 BOND = 1396.5804 ANGLE = 3725.3574 DIHED = 5413.8781 VDWAALS = -3901.2238 EEL = -34651.8749 EGB = -7962.7030 1-4 VDW = 1772.7617 1-4 EEL = 23238.7583 RESTRAINT = 0.0000 ESURF = 189.6920 minimization completed, ENE= -.10778774E+05 RMS= 0.171070E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0712E+04 1.7203E+01 1.2113E+02 CA 2057 BOND = 1439.6180 ANGLE = 3674.6011 DIHED = 5399.6913 VDWAALS = -3885.3068 EEL = -34729.1724 EGB = -7937.6546 1-4 VDW = 1804.4896 1-4 EEL = 23335.3837 RESTRAINT = 0.0000 ESURF = 186.3201 minimization completed, ENE= -.10712030E+05 RMS= 0.172026E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0725E+04 1.7331E+01 1.1248E+02 C 4663 BOND = 1435.0882 ANGLE = 3805.6068 DIHED = 5375.1600 VDWAALS = -3845.1804 EEL = -34944.8930 EGB = -7879.0088 1-4 VDW = 1763.0324 1-4 EEL = 23379.1422 RESTRAINT = 0.0000 ESURF = 186.1013 minimization completed, ENE= -.10724951E+05 RMS= 0.173314E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0842E+04 1.7168E+01 1.2333E+02 C 7074 BOND = 1400.2983 ANGLE = 3648.8695 DIHED = 5354.3276 VDWAALS = -3861.5104 EEL = -34769.7141 EGB = -8015.6342 1-4 VDW = 1820.9133 1-4 EEL = 23391.4850 RESTRAINT = 0.0000 ESURF = 188.4834 minimization completed, ENE= -.10842482E+05 RMS= 0.171678E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0670E+04 1.7266E+01 1.3427E+02 C 986 BOND = 1372.2452 ANGLE = 3727.4860 DIHED = 5407.4978 VDWAALS = -3865.7518 EEL = -34758.4971 EGB = -7859.3905 1-4 VDW = 1822.1276 1-4 EEL = 23296.8820 RESTRAINT = 0.0000 ESURF = 187.7867 minimization completed, ENE= -.10669614E+05 RMS= 0.172658E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0653E+04 1.7584E+01 1.1934E+02 C 1502 BOND = 1440.3529 ANGLE = 3802.5316 DIHED = 5374.7868 VDWAALS = -3898.0543 EEL = -34793.9989 EGB = -7925.2545 1-4 VDW = 1781.7584 1-4 EEL = 23376.8429 RESTRAINT = 0.0000 ESURF = 188.1738 minimization completed, ENE= -.10652861E+05 RMS= 0.175842E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0751E+04 1.7279E+01 1.0671E+02 C 1603 BOND = 1473.7896 ANGLE = 3700.5773 DIHED = 5395.4786 VDWAALS = -3865.6273 EEL = -35018.2780 EGB = -7796.0377 1-4 VDW = 1784.0927 1-4 EEL = 23386.8033 RESTRAINT = 0.0000 ESURF = 188.2632 minimization completed, ENE= -.10750938E+05 RMS= 0.172788E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0715E+04 1.7237E+01 1.1579E+02 CD 6912 BOND = 1432.9592 ANGLE = 3738.3580 DIHED = 5396.8462 VDWAALS = -3908.2852 EEL = -34749.6721 EGB = -7927.5116 1-4 VDW = 1796.1854 1-4 EEL = 23319.7356 RESTRAINT = 0.0000 ESURF = 186.2334 minimization completed, ENE= -.10715151E+05 RMS= 0.172365E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0679E+04 1.7326E+01 1.1874E+02 C 2806 BOND = 1404.0094 ANGLE = 3753.2611 DIHED = 5439.4954 VDWAALS = -3881.7081 EEL = -34931.9781 EGB = -7722.5333 1-4 VDW = 1804.3970 1-4 EEL = 23269.2024 RESTRAINT = 0.0000 ESURF = 187.3142 minimization completed, ENE= -.10678540E+05 RMS= 0.173263E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0656E+04 1.7493E+01 1.1158E+02 CG 1287 BOND = 1465.8010 ANGLE = 3728.6098 DIHED = 5387.1266 VDWAALS = -3871.1419 EEL = -34859.1692 EGB = -7770.5865 1-4 VDW = 1784.2125 1-4 EEL = 23293.5346 RESTRAINT = 0.0000 ESURF = 185.8898 minimization completed, ENE= -.10655723E+05 RMS= 0.174929E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0783E+04 1.7253E+01 1.1420E+02 C 3442 BOND = 1410.2974 ANGLE = 3659.7618 DIHED = 5388.0109 VDWAALS = -3923.6759 EEL = -34791.3183 EGB = -7816.8717 1-4 VDW = 1826.9955 1-4 EEL = 23277.8591 RESTRAINT = 0.0000 ESURF = 185.7907 minimization completed, ENE= -.10783151E+05 RMS= 0.172534E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0641E+04 1.7401E+01 1.1220E+02 C 3107 BOND = 1454.0809 ANGLE = 3785.6284 DIHED = 5412.1202 VDWAALS = -3899.7064 EEL = -34782.9649 EGB = -7845.5202 1-4 VDW = 1763.1652 1-4 EEL = 23286.3704 RESTRAINT = 0.0000 ESURF = 185.3707 minimization completed, ENE= -.10641456E+05 RMS= 0.174008E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0627E+04 1.7358E+01 1.2359E+02 C 6673 BOND = 1459.8310 ANGLE = 3716.1898 DIHED = 5492.2190 VDWAALS = -3902.2194 EEL = -35117.1634 EGB = -7553.7044 1-4 VDW = 1794.4682 1-4 EEL = 23300.0821 RESTRAINT = 0.0000 ESURF = 183.4618 minimization completed, ENE= -.10626835E+05 RMS= 0.173577E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0727E+04 1.7422E+01 1.1422E+02 CA 6281 BOND = 1421.1153 ANGLE = 3762.2852 DIHED = 5418.1785 VDWAALS = -3927.7659 EEL = -35031.9331 EGB = -7648.5489 1-4 VDW = 1794.9842 1-4 EEL = 23300.7154 RESTRAINT = 0.0000 ESURF = 184.4560 minimization completed, ENE= -.10726513E+05 RMS= 0.174219E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0614E+04 1.7580E+01 1.2963E+02 C 673 BOND = 1463.7067 ANGLE = 3808.8667 DIHED = 5403.9469 VDWAALS = -3906.4589 EEL = -35098.3146 EGB = -7617.9200 1-4 VDW = 1812.2063 1-4 EEL = 23335.3995 RESTRAINT = 0.0000 ESURF = 184.4469 minimization completed, ENE= -.10614121E+05 RMS= 0.175802E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0654E+04 1.7606E+01 1.2298E+02 CB 186 BOND = 1453.6923 ANGLE = 3785.7290 DIHED = 5383.3590 VDWAALS = -3943.3336 EEL = -35008.4297 EGB = -7651.7419 1-4 VDW = 1785.0255 1-4 EEL = 23358.0616 RESTRAINT = 0.0000 ESURF = 183.9572 minimization completed, ENE= -.10653681E+05 RMS= 0.176057E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0632E+04 1.7650E+01 1.2486E+02 C 1828 BOND = 1466.4576 ANGLE = 3821.3871 DIHED = 5365.6870 VDWAALS = -3871.8121 EEL = -34965.1473 EGB = -7688.7538 1-4 VDW = 1799.4079 1-4 EEL = 23252.8085 RESTRAINT = 0.0000 ESURF = 187.8133 minimization completed, ENE= -.10632152E+05 RMS= 0.176501E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0767E+04 1.7426E+01 1.1404E+02 CZ 7561 BOND = 1442.4866 ANGLE = 3734.4253 DIHED = 5392.0491 VDWAALS = -3902.2428 EEL = -34932.6510 EGB = -7761.1219 1-4 VDW = 1777.6652 1-4 EEL = 23297.1042 RESTRAINT = 0.0000 ESURF = 185.1848 minimization completed, ENE= -.10767100E+05 RMS= 0.174264E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0780E+04 1.7203E+01 1.0549E+02 C 5728 BOND = 1430.7621 ANGLE = 3708.6883 DIHED = 5451.3537 VDWAALS = -3910.4812 EEL = -34992.9108 EGB = -7707.6140 1-4 VDW = 1785.8499 1-4 EEL = 23269.3467 RESTRAINT = 0.0000 ESURF = 184.8673 minimization completed, ENE= -.10780138E+05 RMS= 0.172028E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 690.12 ( 7.68% of Gen B) | Calc gb diag 5325.39 (59.30% of Gen B) | Calc gb off-diag 2965.42 (33.02% of Gen B) | Gen Born time 8980.93 (100.0% of Nonbo) | Nonbond force 8980.93 (100.0% of Force) | Bond/Angle/Dihedral 7.47 ( 0.08% of Force) | Force time 8988.41 (100.0% of Runmd) | Runmd Time 8988.41 (98.97% of Total) | Other 93.71 ( 1.03% of Total) | Total time 9082.14 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 00:30:19.150 on 10/20/2010 | Setup done at 00:30:23.393 on 10/20/2010 | Run done at 03:01:41.291 on 10/20/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/20/2010 at 00:30:18 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _lig.out.13 |INPCRD: 1XCK_chainA_MGATP_noWAT.inpcrd | PARM: 1XCK_chainA_MGATP_noWAT.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _lig.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 = 09/24/09 Time = 02:43:23 NATOM = 7879 NTYPES = 18 NBONH = 3991 MBONA = 3917 NTHETH = 9115 MTHETA = 5297 NPHIH = 17023 MPHIA = 12427 NHPARM = 0 NPARM = 0 NNB = 43422 NRES = 526 NBONA = 3917 NTHETA = 5297 NPHIA = 12427 NUMBND = 52 NUMANG = 108 NPTRA = 66 NATYP = 36 NPHB = 0 IFBOX = 0 NMXRS = 43 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 567848 | Hollerith 24165 | Integer 1061772 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 8678 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 -1.0747E+04 1.7209E+01 1.0560E+02 CD 6463 BOND = 1415.6977 ANGLE = 3741.6855 DIHED = 5412.3308 VDWAALS = -3914.8441 EEL = -34660.5489 EGB = -8069.1730 1-4 VDW = 1808.8520 1-4 EEL = 23331.0292 RESTRAINT = 0.0000 ESURF = 187.9085 minimization completed, ENE= -.10747062E+05 RMS= 0.172087E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0684E+04 1.7662E+01 1.1139E+02 C 7222 BOND = 1446.2142 ANGLE = 3761.8383 DIHED = 5411.9166 VDWAALS = -3860.5493 EEL = -34674.6360 EGB = -8152.2839 1-4 VDW = 1825.0999 1-4 EEL = 23368.8066 RESTRAINT = 0.0000 ESURF = 189.6673 minimization completed, ENE= -.10683926E+05 RMS= 0.176616E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0721E+04 1.7459E+01 1.1662E+02 C 372 BOND = 1436.1304 ANGLE = 3775.8580 DIHED = 5431.9767 VDWAALS = -3908.8833 EEL = -34575.5871 EGB = -8083.2243 1-4 VDW = 1785.3825 1-4 EEL = 23229.0860 RESTRAINT = 0.0000 ESURF = 187.9740 minimization completed, ENE= -.10721287E+05 RMS= 0.174590E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0866E+04 1.7071E+01 1.2306E+02 C 1852 BOND = 1428.4553 ANGLE = 3649.0446 DIHED = 5397.9966 VDWAALS = -3918.9772 EEL = -34359.1372 EGB = -8359.9862 1-4 VDW = 1767.4730 1-4 EEL = 23339.4210 RESTRAINT = 0.0000 ESURF = 189.3465 minimization completed, ENE= -.10866364E+05 RMS= 0.170711E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0712E+04 1.7348E+01 1.1121E+02 CA 3142 BOND = 1440.1167 ANGLE = 3734.0560 DIHED = 5459.2676 VDWAALS = -3861.1767 EEL = -34676.3775 EGB = -8176.2181 1-4 VDW = 1781.5204 1-4 EEL = 23396.2698 RESTRAINT = 0.0000 ESURF = 190.0733 minimization completed, ENE= -.10712469E+05 RMS= 0.173477E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0766E+04 1.7206E+01 1.3295E+02 C 6239 BOND = 1406.5758 ANGLE = 3740.8799 DIHED = 5423.3649 VDWAALS = -3927.1974 EEL = -34597.9722 EGB = -8147.5806 1-4 VDW = 1788.0395 1-4 EEL = 23359.8431 RESTRAINT = 0.0000 ESURF = 188.5136 minimization completed, ENE= -.10765533E+05 RMS= 0.172063E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0702E+04 1.7328E+01 1.0977E+02 C 5162 BOND = 1409.0572 ANGLE = 3788.4162 DIHED = 5413.9227 VDWAALS = -3905.4558 EEL = -34615.2735 EGB = -8019.9552 1-4 VDW = 1813.2635 1-4 EEL = 23227.2322 RESTRAINT = 0.0000 ESURF = 186.3299 minimization completed, ENE= -.10702463E+05 RMS= 0.173284E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0758E+04 1.7145E+01 1.1018E+02 C 884 BOND = 1345.0966 ANGLE = 3839.4284 DIHED = 5425.2588 VDWAALS = -3875.3911 EEL = -34789.5398 EGB = -8006.2182 1-4 VDW = 1782.2054 1-4 EEL = 23332.2678 RESTRAINT = 0.0000 ESURF = 188.9420 minimization completed, ENE= -.10757950E+05 RMS= 0.171454E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0771E+04 1.7433E+01 1.2106E+02 C 7668 BOND = 1432.8893 ANGLE = 3698.1545 DIHED = 5450.8042 VDWAALS = -3918.8841 EEL = -34861.2880 EGB = -7957.2566 1-4 VDW = 1807.0018 1-4 EEL = 23386.0089 RESTRAINT = 0.0000 ESURF = 191.2456 minimization completed, ENE= -.10771324E+05 RMS= 0.174326E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0695E+04 1.7561E+01 1.1360E+02 C 3442 BOND = 1421.3694 ANGLE = 3798.3524 DIHED = 5411.6240 VDWAALS = -3906.9870 EEL = -34713.9279 EGB = -8044.4881 1-4 VDW = 1804.1060 1-4 EEL = 23345.9552 RESTRAINT = 0.0000 ESURF = 188.8064 minimization completed, ENE= -.10695190E+05 RMS= 0.175614E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0743E+04 1.7350E+01 1.2006E+02 CD 5312 BOND = 1436.4654 ANGLE = 3735.5134 DIHED = 5414.6496 VDWAALS = -3893.0245 EEL = -34666.4431 EGB = -8074.7066 1-4 VDW = 1788.0472 1-4 EEL = 23327.8670 RESTRAINT = 0.0000 ESURF = 188.8674 minimization completed, ENE= -.10742764E+05 RMS= 0.173499E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0804E+04 1.7238E+01 1.2184E+02 C 3061 BOND = 1386.0816 ANGLE = 3705.3163 DIHED = 5370.8260 VDWAALS = -3869.0310 EEL = -34843.0288 EGB = -7953.3330 1-4 VDW = 1804.8657 1-4 EEL = 23406.2728 RESTRAINT = 0.0000 ESURF = 188.1203 minimization completed, ENE= -.10803910E+05 RMS= 0.172376E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0748E+04 1.7350E+01 1.1040E+02 C 4873 BOND = 1415.8784 ANGLE = 3765.9282 DIHED = 5383.1687 VDWAALS = -3882.9607 EEL = -34707.7669 EGB = -7951.4576 1-4 VDW = 1789.3295 1-4 EEL = 23253.7498 RESTRAINT = 0.0000 ESURF = 186.1687 minimization completed, ENE= -.10747962E+05 RMS= 0.173498E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0699E+04 1.7420E+01 9.8915E+01 CA 4320 BOND = 1435.8460 ANGLE = 3760.2145 DIHED = 5404.7501 VDWAALS = -3901.0945 EEL = -34746.9438 EGB = -7999.9229 1-4 VDW = 1795.1294 1-4 EEL = 23364.8394 RESTRAINT = 0.0000 ESURF = 188.4267 minimization completed, ENE= -.10698755E+05 RMS= 0.174203E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0836E+04 1.7172E+01 1.1492E+02 CD 3169 BOND = 1409.5944 ANGLE = 3638.8066 DIHED = 5408.7094 VDWAALS = -3879.7310 EEL = -34914.7030 EGB = -7921.2142 1-4 VDW = 1823.0846 1-4 EEL = 23409.9953 RESTRAINT = 0.0000 ESURF = 189.1573 minimization completed, ENE= -.10836301E+05 RMS= 0.171725E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0837E+04 1.7265E+01 1.1541E+02 C 2767 BOND = 1397.4926 ANGLE = 3673.2018 DIHED = 5373.2526 VDWAALS = -3922.9121 EEL = -34503.9460 EGB = -8173.2567 1-4 VDW = 1802.4462 1-4 EEL = 23327.9264 RESTRAINT = 0.0000 ESURF = 188.3557 minimization completed, ENE= -.10837439E+05 RMS= 0.172647E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0813E+04 1.7388E+01 1.2122E+02 C 7074 BOND = 1438.8572 ANGLE = 3691.8769 DIHED = 5394.3388 VDWAALS = -3899.9657 EEL = -34829.4147 EGB = -7947.4012 1-4 VDW = 1811.3372 1-4 EEL = 23338.5337 RESTRAINT = 0.0000 ESURF = 188.6581 minimization completed, ENE= -.10813180E+05 RMS= 0.173881E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0716E+04 1.7363E+01 1.1740E+02 C 1141 BOND = 1437.4081 ANGLE = 3741.5755 DIHED = 5372.0847 VDWAALS = -3932.4824 EEL = -34721.6477 EGB = -7939.6458 1-4 VDW = 1831.4182 1-4 EEL = 23306.4060 RESTRAINT = 0.0000 ESURF = 188.4048 minimization completed, ENE= -.10716479E+05 RMS= 0.173633E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0641E+04 1.7348E+01 1.2409E+02 CG 4996 BOND = 1416.7841 ANGLE = 3755.8406 DIHED = 5381.3892 VDWAALS = -3864.8508 EEL = -34804.1199 EGB = -7895.3741 1-4 VDW = 1831.3544 1-4 EEL = 23351.5262 RESTRAINT = 0.0000 ESURF = 186.7053 minimization completed, ENE= -.10640745E+05 RMS= 0.173480E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0744E+04 1.7156E+01 1.1160E+02 N 7302 BOND = 1407.8354 ANGLE = 3734.5056 DIHED = 5380.4013 VDWAALS = -3870.0770 EEL = -34799.3890 EGB = -7906.4804 1-4 VDW = 1799.0645 1-4 EEL = 23324.0567 RESTRAINT = 0.0000 ESURF = 186.4871 minimization completed, ENE= -.10743596E+05 RMS= 0.171556E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0698E+04 1.7389E+01 1.2324E+02 C 3891 BOND = 1384.1417 ANGLE = 3719.4907 DIHED = 5429.8399 VDWAALS = -3896.1370 EEL = -34968.1742 EGB = -7890.0108 1-4 VDW = 1865.0813 1-4 EEL = 23470.9580 RESTRAINT = 0.0000 ESURF = 186.5129 minimization completed, ENE= -.10698298E+05 RMS= 0.173886E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0760E+04 1.7019E+01 9.6384E+01 C 2789 BOND = 1382.6284 ANGLE = 3753.5039 DIHED = 5393.2263 VDWAALS = -3850.7652 EEL = -34954.5719 EGB = -7833.7987 1-4 VDW = 1812.5977 1-4 EEL = 23348.1650 RESTRAINT = 0.0000 ESURF = 189.2578 minimization completed, ENE= -.10759757E+05 RMS= 0.170185E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0680E+04 1.7364E+01 1.1102E+02 CG 961 BOND = 1456.1702 ANGLE = 3749.7432 DIHED = 5416.4067 VDWAALS = -3834.5040 EEL = -34959.0215 EGB = -7803.1070 1-4 VDW = 1804.3854 1-4 EEL = 23302.4089 RESTRAINT = 0.0000 ESURF = 187.8361 minimization completed, ENE= -.10679682E+05 RMS= 0.173640E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0757E+04 1.7323E+01 1.0320E+02 CD 6794 BOND = 1438.7406 ANGLE = 3705.7459 DIHED = 5418.7377 VDWAALS = -3887.7014 EEL = -34887.5501 EGB = -7922.2242 1-4 VDW = 1801.2679 1-4 EEL = 23386.9295 RESTRAINT = 0.0000 ESURF = 188.6579 minimization completed, ENE= -.10757396E+05 RMS= 0.173232E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0724E+04 1.7398E+01 1.3306E+02 C 5350 BOND = 1429.8204 ANGLE = 3754.8403 DIHED = 5437.4374 VDWAALS = -3858.5312 EEL = -34903.4696 EGB = -7886.5903 1-4 VDW = 1794.5799 1-4 EEL = 23317.3417 RESTRAINT = 0.0000 ESURF = 190.1647 minimization completed, ENE= -.10724407E+05 RMS= 0.173976E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0813E+04 1.7256E+01 1.2173E+02 CD 4522 BOND = 1374.6727 ANGLE = 3761.7910 DIHED = 5433.4186 VDWAALS = -3875.2822 EEL = -34973.5089 EGB = -7850.9127 1-4 VDW = 1804.1617 1-4 EEL = 23324.1897 RESTRAINT = 0.0000 ESURF = 188.9224 minimization completed, ENE= -.10812548E+05 RMS= 0.172555E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0679E+04 1.7137E+01 1.2390E+02 C 235 BOND = 1462.9345 ANGLE = 3763.9949 DIHED = 5386.2467 VDWAALS = -3910.8318 EEL = -34999.0969 EGB = -7816.2749 1-4 VDW = 1822.7824 1-4 EEL = 23422.6851 RESTRAINT = 0.0000 ESURF = 188.1372 minimization completed, ENE= -.10679423E+05 RMS= 0.171368E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0760E+04 1.7296E+01 1.0241E+02 CA 2624 BOND = 1414.4782 ANGLE = 3760.5052 DIHED = 5395.9889 VDWAALS = -3899.6499 EEL = -34816.5683 EGB = -7909.9292 1-4 VDW = 1784.2868 1-4 EEL = 23321.9109 RESTRAINT = 0.0000 ESURF = 188.7323 minimization completed, ENE= -.10760245E+05 RMS= 0.172962E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0701E+04 1.7209E+01 1.1568E+02 CD 6140 BOND = 1364.2692 ANGLE = 3811.8606 DIHED = 5420.4764 VDWAALS = -3891.1010 EEL = -34810.9048 EGB = -7891.0109 1-4 VDW = 1796.0598 1-4 EEL = 23311.6252 RESTRAINT = 0.0000 ESURF = 187.5335 minimization completed, ENE= -.10701192E+05 RMS= 0.172088E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0730E+04 1.7075E+01 1.0503E+02 C 21 BOND = 1352.7606 ANGLE = 3780.7692 DIHED = 5444.2056 VDWAALS = -3875.4362 EEL = -34880.0009 EGB = -7908.8849 1-4 VDW = 1795.7962 1-4 EEL = 23373.2508 RESTRAINT = 0.0000 ESURF = 187.2077 minimization completed, ENE= -.10730332E+05 RMS= 0.170751E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0675E+04 1.7350E+01 1.1416E+02 CA 3572 BOND = 1408.1797 ANGLE = 3733.7550 DIHED = 5438.8596 VDWAALS = -3852.2347 EEL = -34915.2614 EGB = -7824.6131 1-4 VDW = 1826.0459 1-4 EEL = 23324.4525 RESTRAINT = 0.0000 ESURF = 186.3062 minimization completed, ENE= -.10674510E+05 RMS= 0.173498E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0755E+04 1.7279E+01 1.1828E+02 C 6379 BOND = 1444.7713 ANGLE = 3725.9180 DIHED = 5453.3398 VDWAALS = -3907.2819 EEL = -34653.3913 EGB = -8072.8447 1-4 VDW = 1781.5297 1-4 EEL = 23286.3829 RESTRAINT = 0.0000 ESURF = 186.5575 minimization completed, ENE= -.10755019E+05 RMS= 0.172795E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0661E+04 1.7473E+01 1.1093E+02 C 6482 BOND = 1414.4781 ANGLE = 3808.4873 DIHED = 5423.4902 VDWAALS = -3876.7418 EEL = -34911.8120 EGB = -7858.7797 1-4 VDW = 1803.5268 1-4 EEL = 23348.6593 RESTRAINT = 0.0000 ESURF = 187.2889 minimization completed, ENE= -.10661403E+05 RMS= 0.174735E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0709E+04 1.7343E+01 1.1348E+02 CA 5 BOND = 1409.2207 ANGLE = 3768.0105 DIHED = 5390.9198 VDWAALS = -3837.9610 EEL = -34717.0777 EGB = -8048.9824 1-4 VDW = 1820.8021 1-4 EEL = 23318.3883 RESTRAINT = 0.0000 ESURF = 188.1781 minimization completed, ENE= -.10708502E+05 RMS= 0.173431E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0700E+04 1.7106E+01 1.0817E+02 C 4495 BOND = 1400.1036 ANGLE = 3795.6938 DIHED = 5399.2263 VDWAALS = -3907.8860 EEL = -34712.9802 EGB = -7989.4845 1-4 VDW = 1788.9674 1-4 EEL = 23339.2532 RESTRAINT = 0.0000 ESURF = 187.0527 minimization completed, ENE= -.10700054E+05 RMS= 0.171063E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0813E+04 1.7326E+01 1.2618E+02 C 1215 BOND = 1395.9658 ANGLE = 3720.0097 DIHED = 5396.4251 VDWAALS = -3894.1885 EEL = -34883.3172 EGB = -7885.9681 1-4 VDW = 1810.9862 1-4 EEL = 23340.1347 RESTRAINT = 0.0000 ESURF = 187.1727 minimization completed, ENE= -.10812780E+05 RMS= 0.173258E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0753E+04 1.7388E+01 1.0832E+02 CD 2779 BOND = 1449.6432 ANGLE = 3729.7168 DIHED = 5410.3525 VDWAALS = -3897.5404 EEL = -34757.6189 EGB = -8036.7820 1-4 VDW = 1806.2851 1-4 EEL = 23354.8400 RESTRAINT = 0.0000 ESURF = 188.3324 minimization completed, ENE= -.10752771E+05 RMS= 0.173875E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0616E+04 1.7448E+01 1.2231E+02 C 5350 BOND = 1443.1255 ANGLE = 3758.2113 DIHED = 5426.9986 VDWAALS = -3866.8844 EEL = -34816.1411 EGB = -7961.3077 1-4 VDW = 1799.5294 1-4 EEL = 23413.3340 RESTRAINT = 0.0000 ESURF = 187.1968 minimization completed, ENE= -.10615937E+05 RMS= 0.174482E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0705E+04 1.7398E+01 1.2839E+02 C 278 BOND = 1413.3755 ANGLE = 3786.2755 DIHED = 5424.1990 VDWAALS = -3865.8877 EEL = -34936.2640 EGB = -7855.2773 1-4 VDW = 1805.4052 1-4 EEL = 23335.6170 RESTRAINT = 0.0000 ESURF = 187.8339 minimization completed, ENE= -.10704723E+05 RMS= 0.173977E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0656E+04 1.7263E+01 1.2116E+02 C 2677 BOND = 1395.0674 ANGLE = 3811.6284 DIHED = 5435.5003 VDWAALS = -3891.1201 EEL = -34646.7351 EGB = -7980.3762 1-4 VDW = 1776.6335 1-4 EEL = 23253.6432 RESTRAINT = 0.0000 ESURF = 189.8404 minimization completed, ENE= -.10655918E+05 RMS= 0.172625E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0658E+04 1.7355E+01 1.1459E+02 N 4318 BOND = 1422.1739 ANGLE = 3777.4233 DIHED = 5428.1877 VDWAALS = -3878.0184 EEL = -34601.3145 EGB = -8113.4184 1-4 VDW = 1837.5564 1-4 EEL = 23281.3083 RESTRAINT = 0.0000 ESURF = 187.8422 minimization completed, ENE= -.10658260E+05 RMS= 0.173546E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0631E+04 1.7266E+01 1.2083E+02 CA 6196 BOND = 1408.7968 ANGLE = 3761.2708 DIHED = 5426.2525 VDWAALS = -3846.2064 EEL = -34772.7407 EGB = -7926.0668 1-4 VDW = 1818.9218 1-4 EEL = 23310.9165 RESTRAINT = 0.0000 ESURF = 188.2878 minimization completed, ENE= -.10630568E+05 RMS= 0.172662E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0699E+04 1.7406E+01 1.0443E+02 CA 5479 BOND = 1417.4200 ANGLE = 3712.4690 DIHED = 5421.6052 VDWAALS = -3880.8579 EEL = -34612.4881 EGB = -8144.2570 1-4 VDW = 1796.9507 1-4 EEL = 23402.9792 RESTRAINT = 0.0000 ESURF = 186.8075 minimization completed, ENE= -.10699371E+05 RMS= 0.174059E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0650E+04 1.7397E+01 1.3110E+02 CA 7592 BOND = 1379.9341 ANGLE = 3774.5484 DIHED = 5439.6949 VDWAALS = -3878.3632 EEL = -34785.8347 EGB = -7912.7090 1-4 VDW = 1823.8427 1-4 EEL = 23321.9053 RESTRAINT = 0.0000 ESURF = 187.1855 minimization completed, ENE= -.10649796E+05 RMS= 0.173968E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0752E+04 1.7152E+01 1.0748E+02 C 6053 BOND = 1400.2010 ANGLE = 3735.3530 DIHED = 5469.1417 VDWAALS = -3911.0940 EEL = -34789.0922 EGB = -7924.0530 1-4 VDW = 1781.2735 1-4 EEL = 23299.5140 RESTRAINT = 0.0000 ESURF = 187.0279 minimization completed, ENE= -.10751728E+05 RMS= 0.171523E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0690E+04 1.7284E+01 1.1494E+02 N 4020 BOND = 1430.6693 ANGLE = 3682.7523 DIHED = 5420.3108 VDWAALS = -3926.1540 EEL = -34814.1531 EGB = -7850.1966 1-4 VDW = 1797.7367 1-4 EEL = 23383.8409 RESTRAINT = 0.0000 ESURF = 185.3437 minimization completed, ENE= -.10689850E+05 RMS= 0.172842E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0729E+04 1.7257E+01 1.3806E+02 C 3427 BOND = 1417.3450 ANGLE = 3700.8743 DIHED = 5410.3323 VDWAALS = -3856.6828 EEL = -34702.6766 EGB = -8056.0181 1-4 VDW = 1802.7569 1-4 EEL = 23367.3056 RESTRAINT = 0.0000 ESURF = 187.6372 minimization completed, ENE= -.10729126E+05 RMS= 0.172571E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0711E+04 1.7466E+01 1.3313E+02 CG 2228 BOND = 1421.4497 ANGLE = 3756.0245 DIHED = 5401.6702 VDWAALS = -3899.1461 EEL = -34640.7087 EGB = -8057.0621 1-4 VDW = 1804.7275 1-4 EEL = 23313.7787 RESTRAINT = 0.0000 ESURF = 187.9091 minimization completed, ENE= -.10711357E+05 RMS= 0.174658E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0620E+04 1.7403E+01 1.1658E+02 C 3829 BOND = 1440.2838 ANGLE = 3728.2661 DIHED = 5398.1815 VDWAALS = -3875.7427 EEL = -34451.0747 EGB = -8142.3417 1-4 VDW = 1806.6309 1-4 EEL = 23287.1731 RESTRAINT = 0.0000 ESURF = 189.0732 minimization completed, ENE= -.10619551E+05 RMS= 0.174032E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0644E+04 1.7451E+01 1.1242E+02 CG 1287 BOND = 1423.2459 ANGLE = 3714.3494 DIHED = 5448.6615 VDWAALS = -3831.5483 EEL = -34681.0046 EGB = -8040.2625 1-4 VDW = 1796.7431 1-4 EEL = 23337.6260 RESTRAINT = 0.0000 ESURF = 187.8039 minimization completed, ENE= -.10644386E+05 RMS= 0.174514E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 685.53 ( 7.63% of Gen B) | Calc gb diag 5316.98 (59.20% of Gen B) | Calc gb off-diag 2979.54 (33.17% of Gen B) | Gen Born time 8982.06 (100.0% of Nonbo) | Nonbond force 8982.06 (99.87% of Force) | Bond/Angle/Dihedral 11.09 ( 0.12% of Force) | Other 0.51 ( 0.01% of Force) | Force time 8993.66 (100.0% of Runmd) | Runmd Time 8993.66 (98.84% of Total) | Other 105.13 ( 1.16% of Total) | Total time 9098.81 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 00:30:17.266 on 10/20/2010 | Setup done at 00:30:20.569 on 10/20/2010 | Run done at 03:01:56.075 on 10/20/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/20/2010 at 00:30:18 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _lig.out.12 |INPCRD: 1XCK_chainA_MGATP_noWAT.inpcrd | PARM: 1XCK_chainA_MGATP_noWAT.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _lig.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 = 09/24/09 Time = 02:43:23 NATOM = 7879 NTYPES = 18 NBONH = 3991 MBONA = 3917 NTHETH = 9115 MTHETA = 5297 NPHIH = 17023 MPHIA = 12427 NHPARM = 0 NPARM = 0 NNB = 43422 NRES = 526 NBONA = 3917 NTHETA = 5297 NPHIA = 12427 NUMBND = 52 NUMANG = 108 NPTRA = 66 NATYP = 36 NPHB = 0 IFBOX = 0 NMXRS = 43 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 567848 | Hollerith 24165 | Integer 1061772 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 8678 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 -1.0825E+04 1.7153E+01 1.2984E+02 C 3090 BOND = 1419.9585 ANGLE = 3696.7667 DIHED = 5401.8471 VDWAALS = -3848.1375 EEL = -34952.0372 EGB = -7853.4347 1-4 VDW = 1799.4156 1-4 EEL = 23319.2336 RESTRAINT = 0.0000 ESURF = 191.3918 minimization completed, ENE= -.10824996E+05 RMS= 0.171533E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0792E+04 1.7439E+01 1.1499E+02 CZ 7236 BOND = 1460.6172 ANGLE = 3715.3402 DIHED = 5496.2563 VDWAALS = -3910.0851 EEL = -35037.5469 EGB = -7761.3164 1-4 VDW = 1749.7714 1-4 EEL = 23305.5867 RESTRAINT = 0.0000 ESURF = 189.4561 minimization completed, ENE= -.10791921E+05 RMS= 0.174388E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0710E+04 1.7537E+01 1.2544E+02 C 4649 BOND = 1428.2636 ANGLE = 3692.1988 DIHED = 5440.7613 VDWAALS = -3889.8964 EEL = -35077.6736 EGB = -7643.9801 1-4 VDW = 1828.8518 1-4 EEL = 23326.2514 RESTRAINT = 0.0000 ESURF = 185.1729 minimization completed, ENE= -.10710050E+05 RMS= 0.175368E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0717E+04 1.7269E+01 1.1480E+02 N 6931 BOND = 1409.9423 ANGLE = 3818.4669 DIHED = 5381.5063 VDWAALS = -3891.7189 EEL = -35070.2585 EGB = -7711.5885 1-4 VDW = 1800.3953 1-4 EEL = 23360.0567 RESTRAINT = 0.0000 ESURF = 186.4023 minimization completed, ENE= -.10716796E+05 RMS= 0.172689E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0766E+04 1.7462E+01 1.1438E+02 CG 7090 BOND = 1428.2402 ANGLE = 3744.7112 DIHED = 5407.6819 VDWAALS = -3838.1707 EEL = -35053.4004 EGB = -7784.9409 1-4 VDW = 1789.5742 1-4 EEL = 23352.2302 RESTRAINT = 0.0000 ESURF = 188.3975 minimization completed, ENE= -.10765677E+05 RMS= 0.174618E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0700E+04 1.7354E+01 1.0812E+02 N 6194 BOND = 1399.3058 ANGLE = 3772.4300 DIHED = 5433.4380 VDWAALS = -3877.8080 EEL = -34950.1897 EGB = -7803.8199 1-4 VDW = 1799.6263 1-4 EEL = 23338.5501 RESTRAINT = 0.0000 ESURF = 188.5285 minimization completed, ENE= -.10699939E+05 RMS= 0.173544E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0742E+04 1.7330E+01 1.0933E+02 C 751 BOND = 1423.2359 ANGLE = 3784.2368 DIHED = 5365.2754 VDWAALS = -3864.7941 EEL = -35085.7048 EGB = -7708.8409 1-4 VDW = 1780.1410 1-4 EEL = 23376.3139 RESTRAINT = 0.0000 ESURF = 188.2763 minimization completed, ENE= -.10741861E+05 RMS= 0.173301E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0717E+04 1.7214E+01 1.1836E+02 C 6317 BOND = 1384.7349 ANGLE = 3826.9612 DIHED = 5380.3287 VDWAALS = -3925.1567 EEL = -34958.3914 EGB = -7772.8638 1-4 VDW = 1828.3065 1-4 EEL = 23332.1902 RESTRAINT = 0.0000 ESURF = 187.2758 minimization completed, ENE= -.10716614E+05 RMS= 0.172141E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0697E+04 1.7694E+01 1.1502E+02 N 1327 BOND = 1453.1537 ANGLE = 3788.5140 DIHED = 5427.0289 VDWAALS = -3885.5576 EEL = -35080.1185 EGB = -7679.6648 1-4 VDW = 1787.6450 1-4 EEL = 23306.5111 RESTRAINT = 0.0000 ESURF = 185.9574 minimization completed, ENE= -.10696531E+05 RMS= 0.176937E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0730E+04 1.7304E+01 1.1017E+02 C 3492 BOND = 1396.7264 ANGLE = 3748.0925 DIHED = 5426.3889 VDWAALS = -3888.1351 EEL = -34845.0612 EGB = -7921.8465 1-4 VDW = 1802.4741 1-4 EEL = 23365.7730 RESTRAINT = 0.0000 ESURF = 185.8185 minimization completed, ENE= -.10729770E+05 RMS= 0.173043E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0812E+04 1.7232E+01 1.2860E+02 C 4248 BOND = 1401.6107 ANGLE = 3741.4851 DIHED = 5397.7559 VDWAALS = -3875.0513 EEL = -34843.7706 EGB = -7946.7317 1-4 VDW = 1776.7856 1-4 EEL = 23349.9942 RESTRAINT = 0.0000 ESURF = 185.4431 minimization completed, ENE= -.10812479E+05 RMS= 0.172319E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0733E+04 1.7276E+01 1.2288E+02 C 2041 BOND = 1453.3642 ANGLE = 3666.2817 DIHED = 5406.2786 VDWAALS = -3875.0650 EEL = -34648.0650 EGB = -8114.7374 1-4 VDW = 1795.6102 1-4 EEL = 23395.6861 RESTRAINT = 0.0000 ESURF = 187.7533 minimization completed, ENE= -.10732893E+05 RMS= 0.172763E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0669E+04 1.7439E+01 1.1882E+02 NE 6068 BOND = 1432.2953 ANGLE = 3819.2954 DIHED = 5430.2208 VDWAALS = -3865.1798 EEL = -34633.3226 EGB = -8082.0757 1-4 VDW = 1771.8017 1-4 EEL = 23270.0155 RESTRAINT = 0.0000 ESURF = 188.0697 minimization completed, ENE= -.10668880E+05 RMS= 0.174392E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0653E+04 1.7541E+01 1.0041E+02 CG 2050 BOND = 1452.9520 ANGLE = 3741.8153 DIHED = 5432.0326 VDWAALS = -3861.2564 EEL = -34630.9451 EGB = -8241.3889 1-4 VDW = 1803.2600 1-4 EEL = 23460.6849 RESTRAINT = 0.0000 ESURF = 190.3253 minimization completed, ENE= -.10652520E+05 RMS= 0.175409E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0680E+04 1.7366E+01 1.2296E+02 C 2570 BOND = 1394.9683 ANGLE = 3787.6675 DIHED = 5417.2780 VDWAALS = -3849.7476 EEL = -34732.1877 EGB = -8034.1597 1-4 VDW = 1799.6252 1-4 EEL = 23349.0272 RESTRAINT = 0.0000 ESURF = 188.0162 minimization completed, ENE= -.10679513E+05 RMS= 0.173656E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0817E+04 1.7065E+01 1.2416E+02 CA 4112 BOND = 1381.2948 ANGLE = 3664.1517 DIHED = 5407.3642 VDWAALS = -3907.7769 EEL = -34767.4893 EGB = -8049.4863 1-4 VDW = 1829.4680 1-4 EEL = 23437.4544 RESTRAINT = 0.0000 ESURF = 187.9182 minimization completed, ENE= -.10817101E+05 RMS= 0.170649E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0757E+04 1.7427E+01 1.1412E+02 CG 617 BOND = 1426.3292 ANGLE = 3723.9279 DIHED = 5399.7337 VDWAALS = -3862.4478 EEL = -34923.5452 EGB = -7912.4640 1-4 VDW = 1807.2669 1-4 EEL = 23395.7359 RESTRAINT = 0.0000 ESURF = 188.8344 minimization completed, ENE= -.10756629E+05 RMS= 0.174270E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0778E+04 1.6977E+01 1.0203E+02 C 2514 BOND = 1372.0190 ANGLE = 3754.5980 DIHED = 5443.0721 VDWAALS = -3905.2914 EEL = -34711.0194 EGB = -7979.5823 1-4 VDW = 1767.2433 1-4 EEL = 23292.7135 RESTRAINT = 0.0000 ESURF = 188.2320 minimization completed, ENE= -.10778015E+05 RMS= 0.169773E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0718E+04 1.7223E+01 1.0664E+02 CG 369 BOND = 1395.6544 ANGLE = 3680.6666 DIHED = 5420.7901 VDWAALS = -3882.3660 EEL = -34608.6195 EGB = -8033.0904 1-4 VDW = 1782.6220 1-4 EEL = 23340.3655 RESTRAINT = 0.0000 ESURF = 186.4724 minimization completed, ENE= -.10717505E+05 RMS= 0.172230E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0631E+04 1.7434E+01 1.0390E+02 CA 5150 BOND = 1429.3947 ANGLE = 3806.2245 DIHED = 5409.1150 VDWAALS = -3872.9872 EEL = -34758.7409 EGB = -8031.8813 1-4 VDW = 1817.2058 1-4 EEL = 23383.3341 RESTRAINT = 0.0000 ESURF = 187.3049 minimization completed, ENE= -.10631030E+05 RMS= 0.174340E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0645E+04 1.7584E+01 1.0931E+02 C 4602 BOND = 1502.0332 ANGLE = 3717.7379 DIHED = 5424.2112 VDWAALS = -3879.3645 EEL = -34683.7581 EGB = -8036.3851 1-4 VDW = 1785.6230 1-4 EEL = 23336.9635 RESTRAINT = 0.0000 ESURF = 188.2903 minimization completed, ENE= -.10644649E+05 RMS= 0.175838E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0912E+04 1.7271E+01 1.2852E+02 CD 1153 BOND = 1389.2594 ANGLE = 3624.6052 DIHED = 5386.4732 VDWAALS = -3893.9155 EEL = -34659.9586 EGB = -8146.2660 1-4 VDW = 1850.9785 1-4 EEL = 23347.7370 RESTRAINT = 0.0000 ESURF = 188.9761 minimization completed, ENE= -.10912111E+05 RMS= 0.172712E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0755E+04 1.7363E+01 1.0575E+02 CA 3801 BOND = 1382.6767 ANGLE = 3738.2019 DIHED = 5437.4186 VDWAALS = -3889.2411 EEL = -34533.6102 EGB = -8215.1285 1-4 VDW = 1809.9617 1-4 EEL = 23326.6247 RESTRAINT = 0.0000 ESURF = 188.3695 minimization completed, ENE= -.10754727E+05 RMS= 0.173635E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0600E+04 1.7408E+01 1.0419E+02 C 113 BOND = 1431.4766 ANGLE = 3841.0377 DIHED = 5463.6711 VDWAALS = -3848.8001 EEL = -34803.4355 EGB = -7945.2171 1-4 VDW = 1779.9461 1-4 EEL = 23293.5491 RESTRAINT = 0.0000 ESURF = 187.5297 minimization completed, ENE= -.10600242E+05 RMS= 0.174082E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0720E+04 1.7198E+01 1.1844E+02 C 6389 BOND = 1396.5377 ANGLE = 3805.9788 DIHED = 5420.0309 VDWAALS = -3863.5100 EEL = -34703.5916 EGB = -8120.6304 1-4 VDW = 1773.5896 1-4 EEL = 23382.7962 RESTRAINT = 0.0000 ESURF = 189.1226 minimization completed, ENE= -.10719676E+05 RMS= 0.171981E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0777E+04 1.7206E+01 1.0198E+02 CA 4301 BOND = 1416.9512 ANGLE = 3731.6471 DIHED = 5409.2225 VDWAALS = -3912.7918 EEL = -34634.0339 EGB = -8100.2385 1-4 VDW = 1805.7065 1-4 EEL = 23318.2536 RESTRAINT = 0.0000 ESURF = 188.5317 minimization completed, ENE= -.10776752E+05 RMS= 0.172063E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0673E+04 1.7686E+01 1.3379E+02 CD 2598 BOND = 1430.0653 ANGLE = 3770.6974 DIHED = 5381.7011 VDWAALS = -3866.6844 EEL = -34620.6329 EGB = -8079.9639 1-4 VDW = 1781.4241 1-4 EEL = 23342.3428 RESTRAINT = 0.0000 ESURF = 188.0465 minimization completed, ENE= -.10673004E+05 RMS= 0.176861E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0733E+04 1.7358E+01 1.1544E+02 C 4682 BOND = 1440.6282 ANGLE = 3768.6727 DIHED = 5423.3711 VDWAALS = -3885.0625 EEL = -34507.3103 EGB = -8272.6869 1-4 VDW = 1759.7430 1-4 EEL = 23347.8041 RESTRAINT = 0.0000 ESURF = 191.5758 minimization completed, ENE= -.10733265E+05 RMS= 0.173577E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0720E+04 1.7380E+01 1.2186E+02 C 1742 BOND = 1412.1417 ANGLE = 3669.4261 DIHED = 5436.0493 VDWAALS = -3903.0222 EEL = -34649.8832 EGB = -7994.5693 1-4 VDW = 1810.7793 1-4 EEL = 23308.7004 RESTRAINT = 0.0000 ESURF = 190.0411 minimization completed, ENE= -.10720337E+05 RMS= 0.173795E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0703E+04 1.7424E+01 1.2117E+02 CD 2511 BOND = 1396.6371 ANGLE = 3718.1026 DIHED = 5418.6609 VDWAALS = -3844.2217 EEL = -34726.3250 EGB = -8064.5736 1-4 VDW = 1805.5865 1-4 EEL = 23402.6840 RESTRAINT = 0.0000 ESURF = 190.5387 minimization completed, ENE= -.10702910E+05 RMS= 0.174244E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0682E+04 1.7224E+01 1.0437E+02 NH2 4805 BOND = 1411.8762 ANGLE = 3794.1095 DIHED = 5421.1321 VDWAALS = -3888.2895 EEL = -34609.7577 EGB = -8067.9430 1-4 VDW = 1781.6916 1-4 EEL = 23286.4755 RESTRAINT = 0.0000 ESURF = 188.7204 minimization completed, ENE= -.10681985E+05 RMS= 0.172235E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0670E+04 1.7333E+01 1.1084E+02 CD 3073 BOND = 1409.5032 ANGLE = 3845.6515 DIHED = 5426.2393 VDWAALS = -3889.2221 EEL = -34687.5996 EGB = -8027.1575 1-4 VDW = 1794.1135 1-4 EEL = 23269.8563 RESTRAINT = 0.0000 ESURF = 188.2677 minimization completed, ENE= -.10670348E+05 RMS= 0.173326E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0775E+04 1.7351E+01 1.0445E+02 CD 3439 BOND = 1454.1001 ANGLE = 3732.4212 DIHED = 5401.8031 VDWAALS = -3891.5790 EEL = -34683.6603 EGB = -8133.1405 1-4 VDW = 1772.8776 1-4 EEL = 23383.3279 RESTRAINT = 0.0000 ESURF = 188.7051 minimization completed, ENE= -.10775145E+05 RMS= 0.173508E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0757E+04 1.7167E+01 1.0344E+02 C 5847 BOND = 1389.5809 ANGLE = 3713.0952 DIHED = 5423.6515 VDWAALS = -3884.1904 EEL = -34639.1484 EGB = -8072.3027 1-4 VDW = 1796.5412 1-4 EEL = 23326.8930 RESTRAINT = 0.0000 ESURF = 189.3319 minimization completed, ENE= -.10756548E+05 RMS= 0.171668E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0785E+04 1.7113E+01 1.3174E+02 CA 7470 BOND = 1384.5134 ANGLE = 3672.5078 DIHED = 5401.2103 VDWAALS = -3890.7738 EEL = -34638.0124 EGB = -8072.5580 1-4 VDW = 1797.9973 1-4 EEL = 23370.6824 RESTRAINT = 0.0000 ESURF = 189.7300 minimization completed, ENE= -.10784703E+05 RMS= 0.171132E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0733E+04 1.7216E+01 1.1016E+02 CD 4747 BOND = 1398.7423 ANGLE = 3766.0199 DIHED = 5396.6541 VDWAALS = -3862.9799 EEL = -34639.8766 EGB = -8099.7436 1-4 VDW = 1792.0013 1-4 EEL = 23324.7381 RESTRAINT = 0.0000 ESURF = 190.9835 minimization completed, ENE= -.10733461E+05 RMS= 0.172159E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0714E+04 1.7311E+01 1.1813E+02 N 7634 BOND = 1416.1073 ANGLE = 3769.9139 DIHED = 5368.5486 VDWAALS = -3838.7331 EEL = -34678.3552 EGB = -8065.5479 1-4 VDW = 1799.5675 1-4 EEL = 23325.6214 RESTRAINT = 0.0000 ESURF = 189.1168 minimization completed, ENE= -.10713761E+05 RMS= 0.173111E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0663E+04 1.7570E+01 1.3344E+02 C 7788 BOND = 1438.9069 ANGLE = 3796.0725 DIHED = 5462.2479 VDWAALS = -3870.0847 EEL = -34619.9951 EGB = -8164.6984 1-4 VDW = 1789.2132 1-4 EEL = 23313.4655 RESTRAINT = 0.0000 ESURF = 192.1820 minimization completed, ENE= -.10662690E+05 RMS= 0.175698E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0691E+04 1.7515E+01 1.3335E+02 CZ 2965 BOND = 1453.1102 ANGLE = 3778.3687 DIHED = 5424.8436 VDWAALS = -3898.7459 EEL = -34605.7499 EGB = -8263.9973 1-4 VDW = 1799.8666 1-4 EEL = 23430.2080 RESTRAINT = 0.0000 ESURF = 191.1462 minimization completed, ENE= -.10690950E+05 RMS= 0.175147E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0772E+04 1.7485E+01 1.1394E+02 CA 907 BOND = 1449.9752 ANGLE = 3711.4839 DIHED = 5391.0591 VDWAALS = -3884.2579 EEL = -34814.2496 EGB = -8054.8443 1-4 VDW = 1808.9116 1-4 EEL = 23430.2319 RESTRAINT = 0.0000 ESURF = 189.2039 minimization completed, ENE= -.10772486E+05 RMS= 0.174850E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0691E+04 1.7344E+01 1.0477E+02 C 7800 BOND = 1385.5313 ANGLE = 3781.1013 DIHED = 5452.6068 VDWAALS = -3906.8917 EEL = -34732.1409 EGB = -8099.5478 1-4 VDW = 1824.7773 1-4 EEL = 23413.9495 RESTRAINT = 0.0000 ESURF = 189.8585 minimization completed, ENE= -.10690756E+05 RMS= 0.173438E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0898E+04 1.7165E+01 1.0499E+02 C 2926 BOND = 1420.0811 ANGLE = 3650.9600 DIHED = 5411.4248 VDWAALS = -3892.2057 EEL = -34772.2989 EGB = -8077.9935 1-4 VDW = 1795.2325 1-4 EEL = 23376.2629 RESTRAINT = 0.0000 ESURF = 190.5505 minimization completed, ENE= -.10897986E+05 RMS= 0.171651E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0730E+04 1.7294E+01 1.0942E+02 C 4130 BOND = 1471.4235 ANGLE = 3756.6455 DIHED = 5407.7467 VDWAALS = -3822.2032 EEL = -34845.3415 EGB = -8011.8177 1-4 VDW = 1775.5279 1-4 EEL = 23346.5895 RESTRAINT = 0.0000 ESURF = 191.2185 minimization completed, ENE= -.10730211E+05 RMS= 0.172937E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0755E+04 1.7368E+01 1.2653E+02 C 6150 BOND = 1458.6648 ANGLE = 3695.7067 DIHED = 5411.1805 VDWAALS = -3838.6003 EEL = -34594.0852 EGB = -8176.4394 1-4 VDW = 1775.8055 1-4 EEL = 23320.4930 RESTRAINT = 0.0000 ESURF = 191.8309 minimization completed, ENE= -.10755444E+05 RMS= 0.173676E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0726E+04 1.7318E+01 1.2144E+02 C 1052 BOND = 1442.7974 ANGLE = 3677.6599 DIHED = 5427.2033 VDWAALS = -3798.3784 EEL = -34550.0885 EGB = -8307.7569 1-4 VDW = 1815.7274 1-4 EEL = 23373.9334 RESTRAINT = 0.0000 ESURF = 193.0407 minimization completed, ENE= -.10725862E+05 RMS= 0.173178E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0723E+04 1.7243E+01 1.0763E+02 CZ 862 BOND = 1401.8797 ANGLE = 3746.2509 DIHED = 5448.1755 VDWAALS = -3849.1328 EEL = -34852.0911 EGB = -7999.6288 1-4 VDW = 1825.1887 1-4 EEL = 23367.4742 RESTRAINT = 0.0000 ESURF = 189.0235 minimization completed, ENE= -.10722860E+05 RMS= 0.172431E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0770E+04 1.7367E+01 1.1041E+02 CD 2701 BOND = 1396.7045 ANGLE = 3732.3467 DIHED = 5375.7943 VDWAALS = -3868.9866 EEL = -34711.0920 EGB = -8012.9035 1-4 VDW = 1790.4006 1-4 EEL = 23336.9779 RESTRAINT = 0.0000 ESURF = 191.1481 minimization completed, ENE= -.10769610E+05 RMS= 0.173673E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0871E+04 1.6999E+01 1.1818E+02 CZ 2900 BOND = 1364.7213 ANGLE = 3660.9347 DIHED = 5434.8271 VDWAALS = -3865.2943 EEL = -34670.5478 EGB = -8104.0452 1-4 VDW = 1797.9165 1-4 EEL = 23321.3705 RESTRAINT = 0.0000 ESURF = 189.4338 minimization completed, ENE= -.10870683E+05 RMS= 0.169988E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0829E+04 1.7243E+01 1.2056E+02 CG 782 BOND = 1412.4642 ANGLE = 3702.7238 DIHED = 5443.9602 VDWAALS = -3866.8402 EEL = -34798.1651 EGB = -7974.7540 1-4 VDW = 1770.4418 1-4 EEL = 23292.1488 RESTRAINT = 0.0000 ESURF = 189.5101 minimization completed, ENE= -.10828510E+05 RMS= 0.172428E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0721E+04 1.7290E+01 1.1284E+02 CG 369 BOND = 1414.9250 ANGLE = 3714.5969 DIHED = 5423.7685 VDWAALS = -3840.7809 EEL = -34732.6203 EGB = -8018.2984 1-4 VDW = 1803.8334 1-4 EEL = 23325.6556 RESTRAINT = 0.0000 ESURF = 188.2683 minimization completed, ENE= -.10720652E+05 RMS= 0.172902E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 680.58 ( 7.57% of Gen B) | Calc gb diag 5330.64 (59.30% of Gen B) | Calc gb off-diag 2978.65 (33.13% of Gen B) | Gen Born time 8989.87 (100.0% of Nonbo) | Nonbond force 8989.87 (100.0% of Force) | Bond/Angle/Dihedral 4.97 ( 0.06% of Force) | Force time 8994.85 (100.0% of Runmd) | Runmd Time 8994.85 (99.05% of Total) | Other 85.82 ( 0.95% of Total) | Total time 9080.69 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 00:30:17.264 on 10/20/2010 | Setup done at 00:30:20.169 on 10/20/2010 | Run done at 03:01:37.953 on 10/20/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/20/2010 at 00:30:17 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _lig.out.11 |INPCRD: 1XCK_chainA_MGATP_noWAT.inpcrd | PARM: 1XCK_chainA_MGATP_noWAT.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _lig.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 = 09/24/09 Time = 02:43:23 NATOM = 7879 NTYPES = 18 NBONH = 3991 MBONA = 3917 NTHETH = 9115 MTHETA = 5297 NPHIH = 17023 MPHIA = 12427 NHPARM = 0 NPARM = 0 NNB = 43422 NRES = 526 NBONA = 3917 NTHETA = 5297 NPHIA = 12427 NUMBND = 52 NUMANG = 108 NPTRA = 66 NATYP = 36 NPHB = 0 IFBOX = 0 NMXRS = 43 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 567848 | Hollerith 24165 | Integer 1061772 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 8678 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 -1.0821E+04 1.7222E+01 1.1316E+02 C 1842 BOND = 1395.9339 ANGLE = 3659.0398 DIHED = 5387.3256 VDWAALS = -3855.1636 EEL = -34995.0424 EGB = -7822.8967 1-4 VDW = 1813.8252 1-4 EEL = 23410.0932 RESTRAINT = 0.0000 ESURF = 186.2026 minimization completed, ENE= -.10820682E+05 RMS= 0.172223E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0667E+04 1.7311E+01 1.0801E+02 CG 1777 BOND = 1400.0471 ANGLE = 3837.7853 DIHED = 5392.2191 VDWAALS = -3842.4473 EEL = -34986.1773 EGB = -7784.7049 1-4 VDW = 1822.7534 1-4 EEL = 23306.4889 RESTRAINT = 0.0000 ESURF = 187.4272 minimization completed, ENE= -.10666608E+05 RMS= 0.173107E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0639E+04 1.7341E+01 1.1207E+02 CB 5291 BOND = 1472.7198 ANGLE = 3780.4550 DIHED = 5406.3698 VDWAALS = -3832.8827 EEL = -34896.3914 EGB = -7841.1324 1-4 VDW = 1792.6778 1-4 EEL = 23290.4570 RESTRAINT = 0.0000 ESURF = 188.2293 minimization completed, ENE= -.10639498E+05 RMS= 0.173410E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0736E+04 1.7314E+01 1.0845E+02 C 5266 BOND = 1454.7083 ANGLE = 3743.0565 DIHED = 5436.7882 VDWAALS = -3888.7659 EEL = -34787.0652 EGB = -7901.8638 1-4 VDW = 1768.7224 1-4 EEL = 23249.1714 RESTRAINT = 0.0000 ESURF = 189.2838 minimization completed, ENE= -.10735964E+05 RMS= 0.173139E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0639E+04 1.7416E+01 1.1610E+02 C 7300 BOND = 1437.5206 ANGLE = 3785.8554 DIHED = 5413.1662 VDWAALS = -3864.6870 EEL = -34728.9217 EGB = -7993.1695 1-4 VDW = 1804.8127 1-4 EEL = 23320.1720 RESTRAINT = 0.0000 ESURF = 186.7124 minimization completed, ENE= -.10638539E+05 RMS= 0.174164E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0702E+04 1.7373E+01 1.1645E+02 C 146 BOND = 1410.9942 ANGLE = 3794.3954 DIHED = 5405.6753 VDWAALS = -3877.7515 EEL = -34925.8281 EGB = -7837.7081 1-4 VDW = 1789.1321 1-4 EEL = 23350.1383 RESTRAINT = 0.0000 ESURF = 188.8487 minimization completed, ENE= -.10702104E+05 RMS= 0.173733E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0711E+04 1.7282E+01 1.1102E+02 N 4020 BOND = 1476.2173 ANGLE = 3699.1049 DIHED = 5426.4928 VDWAALS = -3918.3653 EEL = -34860.3074 EGB = -7815.8501 1-4 VDW = 1807.4261 1-4 EEL = 23287.3129 RESTRAINT = 0.0000 ESURF = 186.7444 minimization completed, ENE= -.10711225E+05 RMS= 0.172818E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0734E+04 1.7434E+01 1.2614E+02 C 3370 BOND = 1431.9281 ANGLE = 3822.3678 DIHED = 5412.1057 VDWAALS = -3903.1491 EEL = -34974.3299 EGB = -7796.9652 1-4 VDW = 1785.2654 1-4 EEL = 23301.0410 RESTRAINT = 0.0000 ESURF = 187.4728 minimization completed, ENE= -.10734263E+05 RMS= 0.174337E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0663E+04 1.7331E+01 1.1572E+02 CD 4328 BOND = 1385.6762 ANGLE = 3862.9676 DIHED = 5427.2692 VDWAALS = -3868.8281 EEL = -34755.5476 EGB = -7981.0553 1-4 VDW = 1776.6604 1-4 EEL = 23300.1204 RESTRAINT = 0.0000 ESURF = 189.7104 minimization completed, ENE= -.10663027E+05 RMS= 0.173307E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0757E+04 1.7052E+01 1.0893E+02 CZ 6070 BOND = 1384.3583 ANGLE = 3796.0396 DIHED = 5433.3428 VDWAALS = -3895.1111 EEL = -34956.3856 EGB = -7811.9491 1-4 VDW = 1803.4938 1-4 EEL = 23302.9124 RESTRAINT = 0.0000 ESURF = 186.0403 minimization completed, ENE= -.10757258E+05 RMS= 0.170515E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0776E+04 1.7157E+01 1.0505E+02 CG2 2582 BOND = 1437.3480 ANGLE = 3696.3919 DIHED = 5443.1050 VDWAALS = -3904.7095 EEL = -34991.9910 EGB = -7748.9503 1-4 VDW = 1812.5128 1-4 EEL = 23295.3042 RESTRAINT = 0.0000 ESURF = 185.4866 minimization completed, ENE= -.10775502E+05 RMS= 0.171566E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0635E+04 1.7217E+01 1.2916E+02 C 196 BOND = 1356.9938 ANGLE = 3848.1702 DIHED = 5444.8697 VDWAALS = -3887.8855 EEL = -34780.1867 EGB = -7919.4291 1-4 VDW = 1821.9866 1-4 EEL = 23294.0800 RESTRAINT = 0.0000 ESURF = 186.6648 minimization completed, ENE= -.10634736E+05 RMS= 0.172173E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0783E+04 1.7148E+01 1.2559E+02 CG 2852 BOND = 1371.8358 ANGLE = 3747.7919 DIHED = 5418.1581 VDWAALS = -3922.1251 EEL = -34774.3184 EGB = -7919.4104 1-4 VDW = 1799.6454 1-4 EEL = 23310.0556 RESTRAINT = 0.0000 ESURF = 185.4381 minimization completed, ENE= -.10782929E+05 RMS= 0.171478E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0777E+04 1.7319E+01 1.1914E+02 C 7625 BOND = 1417.6018 ANGLE = 3765.4744 DIHED = 5382.6840 VDWAALS = -3884.6460 EEL = -34840.2955 EGB = -7932.6111 1-4 VDW = 1808.7085 1-4 EEL = 23320.6844 RESTRAINT = 0.0000 ESURF = 185.8502 minimization completed, ENE= -.10776549E+05 RMS= 0.173192E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0703E+04 1.7393E+01 1.1469E+02 CG 7153 BOND = 1403.7822 ANGLE = 3788.9599 DIHED = 5391.3702 VDWAALS = -3870.6317 EEL = -34759.6808 EGB = -7976.5181 1-4 VDW = 1798.2163 1-4 EEL = 23336.3772 RESTRAINT = 0.0000 ESURF = 185.4764 minimization completed, ENE= -.10702648E+05 RMS= 0.173927E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0752E+04 1.7437E+01 1.1907E+02 C 1677 BOND = 1416.6994 ANGLE = 3689.1626 DIHED = 5349.5398 VDWAALS = -3917.7866 EEL = -34687.3791 EGB = -7915.7386 1-4 VDW = 1829.9686 1-4 EEL = 23299.6623 RESTRAINT = 0.0000 ESURF = 184.1670 minimization completed, ENE= -.10751705E+05 RMS= 0.174370E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0666E+04 1.7231E+01 1.1757E+02 C 3123 BOND = 1386.4713 ANGLE = 3741.0577 DIHED = 5438.6045 VDWAALS = -3911.3661 EEL = -34823.3986 EGB = -7855.6106 1-4 VDW = 1839.6483 1-4 EEL = 23333.9246 RESTRAINT = 0.0000 ESURF = 184.5846 minimization completed, ENE= -.10666084E+05 RMS= 0.172306E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0822E+04 1.7095E+01 1.0964E+02 C 3459 BOND = 1369.5738 ANGLE = 3761.7642 DIHED = 5393.9612 VDWAALS = -3913.8532 EEL = -34822.1102 EGB = -7791.8816 1-4 VDW = 1778.1937 1-4 EEL = 23216.8918 RESTRAINT = 0.0000 ESURF = 185.0738 minimization completed, ENE= -.10822387E+05 RMS= 0.170950E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0699E+04 1.7279E+01 1.2306E+02 N 2434 BOND = 1423.2995 ANGLE = 3758.2390 DIHED = 5386.9717 VDWAALS = -3912.0568 EEL = -34835.9348 EGB = -7885.9143 1-4 VDW = 1807.4708 1-4 EEL = 23372.2485 RESTRAINT = 0.0000 ESURF = 186.3209 minimization completed, ENE= -.10699356E+05 RMS= 0.172794E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0748E+04 1.7236E+01 1.1490E+02 CD 5041 BOND = 1409.5970 ANGLE = 3711.3992 DIHED = 5376.2480 VDWAALS = -3907.6355 EEL = -34751.4200 EGB = -7880.0724 1-4 VDW = 1797.5035 1-4 EEL = 23310.1067 RESTRAINT = 0.0000 ESURF = 186.2048 minimization completed, ENE= -.10748069E+05 RMS= 0.172358E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0702E+04 1.7477E+01 1.2317E+02 C 5069 BOND = 1483.0364 ANGLE = 3740.1442 DIHED = 5418.4472 VDWAALS = -3915.0587 EEL = -34755.3549 EGB = -7948.1563 1-4 VDW = 1779.0906 1-4 EEL = 23307.8303 RESTRAINT = 0.0000 ESURF = 187.6687 minimization completed, ENE= -.10702353E+05 RMS= 0.174769E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0707E+04 1.7446E+01 1.2904E+02 CA 7148 BOND = 1449.0119 ANGLE = 3829.0925 DIHED = 5378.1649 VDWAALS = -3859.8745 EEL = -35044.6513 EGB = -7698.2824 1-4 VDW = 1765.4433 1-4 EEL = 23285.5759 RESTRAINT = 0.0000 ESURF = 188.0748 minimization completed, ENE= -.10707445E+05 RMS= 0.174461E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0708E+04 1.7396E+01 1.1571E+02 C 5598 BOND = 1422.8510 ANGLE = 3814.5216 DIHED = 5367.5163 VDWAALS = -3916.9200 EEL = -34820.4867 EGB = -7862.8574 1-4 VDW = 1776.9254 1-4 EEL = 23322.2419 RESTRAINT = 0.0000 ESURF = 188.0104 minimization completed, ENE= -.10708198E+05 RMS= 0.173965E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0683E+04 1.7395E+01 1.1124E+02 CE 1543 BOND = 1411.1836 ANGLE = 3859.5802 DIHED = 5391.3855 VDWAALS = -3853.3598 EEL = -34885.8514 EGB = -7840.4048 1-4 VDW = 1770.9217 1-4 EEL = 23275.4609 RESTRAINT = 0.0000 ESURF = 187.9375 minimization completed, ENE= -.10683147E+05 RMS= 0.173953E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0660E+04 1.7429E+01 1.1148E+02 CD 949 BOND = 1447.4912 ANGLE = 3809.3991 DIHED = 5367.8543 VDWAALS = -3903.1500 EEL = -34951.1361 EGB = -7794.0789 1-4 VDW = 1808.0382 1-4 EEL = 23367.5396 RESTRAINT = 0.0000 ESURF = 188.1361 minimization completed, ENE= -.10659907E+05 RMS= 0.174294E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0761E+04 1.7505E+01 1.0495E+02 N 1341 BOND = 1454.1601 ANGLE = 3728.4519 DIHED = 5393.4443 VDWAALS = -3927.8070 EEL = -34846.6321 EGB = -7804.8822 1-4 VDW = 1801.8755 1-4 EEL = 23254.0691 RESTRAINT = 0.0000 ESURF = 185.9456 minimization completed, ENE= -.10761375E+05 RMS= 0.175049E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0734E+04 1.7484E+01 1.1090E+02 C 2767 BOND = 1421.3821 ANGLE = 3768.4679 DIHED = 5427.8180 VDWAALS = -3883.6036 EEL = -35164.6437 EGB = -7686.7284 1-4 VDW = 1778.2511 1-4 EEL = 23418.6490 RESTRAINT = 0.0000 ESURF = 186.7270 minimization completed, ENE= -.10733681E+05 RMS= 0.174839E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0807E+04 1.7200E+01 1.0680E+02 C 2879 BOND = 1367.9814 ANGLE = 3743.8386 DIHED = 5379.0544 VDWAALS = -3879.0521 EEL = -35127.2820 EGB = -7628.2025 1-4 VDW = 1803.9624 1-4 EEL = 23347.5576 RESTRAINT = 0.0000 ESURF = 185.0607 minimization completed, ENE= -.10807082E+05 RMS= 0.172002E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0800E+04 1.7314E+01 1.1416E+02 C 1103 BOND = 1407.2985 ANGLE = 3701.0276 DIHED = 5416.3713 VDWAALS = -3890.5409 EEL = -34828.1272 EGB = -7879.5388 1-4 VDW = 1822.9351 1-4 EEL = 23264.3272 RESTRAINT = 0.0000 ESURF = 186.4764 minimization completed, ENE= -.10799771E+05 RMS= 0.173136E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0849E+04 1.7167E+01 1.3046E+02 CD 3816 BOND = 1383.5234 ANGLE = 3720.5957 DIHED = 5405.5849 VDWAALS = -3877.0130 EEL = -34856.6182 EGB = -7881.0856 1-4 VDW = 1819.2433 1-4 EEL = 23250.7032 RESTRAINT = 0.0000 ESURF = 186.3169 minimization completed, ENE= -.10848749E+05 RMS= 0.171665E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0843E+04 1.6989E+01 1.3036E+02 CG 782 BOND = 1336.8689 ANGLE = 3785.0578 DIHED = 5395.1198 VDWAALS = -3922.8641 EEL = -34967.3667 EGB = -7781.4146 1-4 VDW = 1793.0913 1-4 EEL = 23331.7698 RESTRAINT = 0.0000 ESURF = 186.5394 minimization completed, ENE= -.10843198E+05 RMS= 0.169892E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0889E+04 1.7136E+01 1.0389E+02 N 1071 BOND = 1425.9400 ANGLE = 3701.6244 DIHED = 5396.7830 VDWAALS = -3888.9218 EEL = -34978.2937 EGB = -7824.7944 1-4 VDW = 1781.0742 1-4 EEL = 23310.7651 RESTRAINT = 0.0000 ESURF = 186.4315 minimization completed, ENE= -.10889392E+05 RMS= 0.171357E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0744E+04 1.7418E+01 1.1759E+02 C 6097 BOND = 1468.8301 ANGLE = 3710.5457 DIHED = 5445.7525 VDWAALS = -3892.1801 EEL = -34900.5917 EGB = -7791.6077 1-4 VDW = 1792.8942 1-4 EEL = 23236.9359 RESTRAINT = 0.0000 ESURF = 185.0075 minimization completed, ENE= -.10744414E+05 RMS= 0.174180E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0763E+04 1.7196E+01 1.0416E+02 N 1456 BOND = 1407.2470 ANGLE = 3810.9472 DIHED = 5359.1687 VDWAALS = -3889.2765 EEL = -34888.3488 EGB = -7917.9074 1-4 VDW = 1811.8867 1-4 EEL = 23356.4978 RESTRAINT = 0.0000 ESURF = 186.7681 minimization completed, ENE= -.10763017E+05 RMS= 0.171961E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0834E+04 1.7227E+01 1.0769E+02 CD 6712 BOND = 1393.6788 ANGLE = 3673.6721 DIHED = 5403.6097 VDWAALS = -3911.0710 EEL = -34889.6038 EGB = -7930.3132 1-4 VDW = 1818.0986 1-4 EEL = 23421.4670 RESTRAINT = 0.0000 ESURF = 186.4430 minimization completed, ENE= -.10834019E+05 RMS= 0.172268E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0785E+04 1.7257E+01 9.9203E+01 CD 6140 BOND = 1384.4895 ANGLE = 3760.0725 DIHED = 5421.5623 VDWAALS = -3879.1921 EEL = -34899.9597 EGB = -7922.0833 1-4 VDW = 1796.1283 1-4 EEL = 23367.9784 RESTRAINT = 0.0000 ESURF = 185.9076 minimization completed, ENE= -.10785096E+05 RMS= 0.172574E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0773E+04 1.7295E+01 1.2322E+02 CA 4899 BOND = 1397.8344 ANGLE = 3724.5782 DIHED = 5414.2084 VDWAALS = -3912.5755 EEL = -34802.6768 EGB = -7922.2547 1-4 VDW = 1799.5300 1-4 EEL = 23340.8921 RESTRAINT = 0.0000 ESURF = 187.0522 minimization completed, ENE= -.10773412E+05 RMS= 0.172953E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0683E+04 1.7422E+01 1.1346E+02 C 6206 BOND = 1437.4273 ANGLE = 3833.6552 DIHED = 5426.9614 VDWAALS = -3867.7683 EEL = -35088.4235 EGB = -7814.5092 1-4 VDW = 1812.5716 1-4 EEL = 23390.5250 RESTRAINT = 0.0000 ESURF = 186.1132 minimization completed, ENE= -.10683447E+05 RMS= 0.174218E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0750E+04 1.7482E+01 1.1769E+02 C 4824 BOND = 1470.2261 ANGLE = 3685.8020 DIHED = 5395.7681 VDWAALS = -3871.9074 EEL = -34827.5642 EGB = -7907.8900 1-4 VDW = 1817.4062 1-4 EEL = 23301.6597 RESTRAINT = 0.0000 ESURF = 186.0886 minimization completed, ENE= -.10750411E+05 RMS= 0.174823E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0803E+04 1.6992E+01 1.2091E+02 CE2 4177 BOND = 1413.2077 ANGLE = 3776.9847 DIHED = 5366.8996 VDWAALS = -3903.4879 EEL = -34933.7936 EGB = -7868.9484 1-4 VDW = 1795.4856 1-4 EEL = 23360.9841 RESTRAINT = 0.0000 ESURF = 189.8668 minimization completed, ENE= -.10802801E+05 RMS= 0.169918E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0734E+04 1.7211E+01 1.2132E+02 N 2098 BOND = 1408.5036 ANGLE = 3740.9324 DIHED = 5377.8948 VDWAALS = -3891.7556 EEL = -34882.0110 EGB = -7860.7576 1-4 VDW = 1794.3818 1-4 EEL = 23390.7939 RESTRAINT = 0.0000 ESURF = 188.3698 minimization completed, ENE= -.10733648E+05 RMS= 0.172107E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0868E+04 1.7126E+01 1.1004E+02 C 1487 BOND = 1397.6494 ANGLE = 3718.6913 DIHED = 5406.5260 VDWAALS = -3929.2037 EEL = -34993.8881 EGB = -7768.5225 1-4 VDW = 1790.1901 1-4 EEL = 23323.1536 RESTRAINT = 0.0000 ESURF = 187.5478 minimization completed, ENE= -.10867856E+05 RMS= 0.171262E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0720E+04 1.7415E+01 1.2252E+02 CE2 109 BOND = 1449.7426 ANGLE = 3778.3109 DIHED = 5375.9604 VDWAALS = -3893.3088 EEL = -35021.3153 EGB = -7806.2495 1-4 VDW = 1801.2883 1-4 EEL = 23409.5556 RESTRAINT = 0.0000 ESURF = 185.5553 minimization completed, ENE= -.10720461E+05 RMS= 0.174150E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0660E+04 1.7642E+01 1.1003E+02 CG 2253 BOND = 1486.0447 ANGLE = 3838.0362 DIHED = 5419.2097 VDWAALS = -3949.8549 EEL = -34798.1406 EGB = -7867.8019 1-4 VDW = 1773.9535 1-4 EEL = 23250.4728 RESTRAINT = 0.0000 ESURF = 187.6377 minimization completed, ENE= -.10660443E+05 RMS= 0.176423E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0652E+04 1.7518E+01 1.5543E+02 CZ 5225 BOND = 1432.2620 ANGLE = 3743.5634 DIHED = 5482.0296 VDWAALS = -3828.0016 EEL = -34942.6967 EGB = -7777.8175 1-4 VDW = 1807.3540 1-4 EEL = 23241.9988 RESTRAINT = 0.0000 ESURF = 188.9763 minimization completed, ENE= -.10652332E+05 RMS= 0.175182E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0784E+04 1.7393E+01 1.0594E+02 N 3909 BOND = 1438.1196 ANGLE = 3751.8804 DIHED = 5401.8214 VDWAALS = -3922.8998 EEL = -34952.4561 EGB = -7772.9186 1-4 VDW = 1781.7435 1-4 EEL = 23303.1265 RESTRAINT = 0.0000 ESURF = 187.2893 minimization completed, ENE= -.10784294E+05 RMS= 0.173926E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0810E+04 1.7287E+01 1.4290E+02 C 2514 BOND = 1367.3410 ANGLE = 3728.2856 DIHED = 5406.0085 VDWAALS = -3867.8725 EEL = -35005.3153 EGB = -7740.3425 1-4 VDW = 1797.9346 1-4 EEL = 23315.4280 RESTRAINT = 0.0000 ESURF = 188.1944 minimization completed, ENE= -.10810338E+05 RMS= 0.172869E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0699E+04 1.7522E+01 1.0954E+02 CG 1287 BOND = 1423.9531 ANGLE = 3720.1305 DIHED = 5425.8994 VDWAALS = -3819.0129 EEL = -34941.2380 EGB = -7798.9134 1-4 VDW = 1802.1437 1-4 EEL = 23300.4382 RESTRAINT = 0.0000 ESURF = 187.5682 minimization completed, ENE= -.10699031E+05 RMS= 0.175221E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0718E+04 1.7399E+01 1.3535E+02 C 1119 BOND = 1424.5840 ANGLE = 3782.9159 DIHED = 5388.3118 VDWAALS = -3849.6207 EEL = -35042.8181 EGB = -7733.3747 1-4 VDW = 1796.2683 1-4 EEL = 23326.8142 RESTRAINT = 0.0000 ESURF = 188.9675 minimization completed, ENE= -.10717952E+05 RMS= 0.173986E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0834E+04 1.7498E+01 1.0663E+02 C 903 BOND = 1427.3625 ANGLE = 3703.9059 DIHED = 5402.9947 VDWAALS = -3887.0681 EEL = -35059.0774 EGB = -7733.9468 1-4 VDW = 1824.6794 1-4 EEL = 23297.2895 RESTRAINT = 0.0000 ESURF = 189.9827 minimization completed, ENE= -.10833878E+05 RMS= 0.174983E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 684.88 ( 7.63% of Gen B) | Calc gb diag 5316.23 (59.23% of Gen B) | Calc gb off-diag 2973.55 (33.13% of Gen B) | Other 0.50 ( 0.01% of Gen B) | Gen Born time 8975.17 (100.0% of Nonbo) | Nonbond force 8975.17 (100.0% of Force) | Bond/Angle/Dihedral 6.16 ( 0.07% of Force) | Force time 8981.33 (100.0% of Runmd) | Runmd Time 8981.33 (99.02% of Total) | Other 89.25 ( 0.98% of Total) | Total time 9070.60 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 00:30:16.928 on 10/20/2010 | Setup done at 00:30:18.711 on 10/20/2010 | Run done at 03:01:27.528 on 10/20/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/20/2010 at 00:30:19 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _lig.out.10 |INPCRD: 1XCK_chainA_MGATP_noWAT.inpcrd | PARM: 1XCK_chainA_MGATP_noWAT.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _lig.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 = 09/24/09 Time = 02:43:23 NATOM = 7879 NTYPES = 18 NBONH = 3991 MBONA = 3917 NTHETH = 9115 MTHETA = 5297 NPHIH = 17023 MPHIA = 12427 NHPARM = 0 NPARM = 0 NNB = 43422 NRES = 526 NBONA = 3917 NTHETA = 5297 NPHIA = 12427 NUMBND = 52 NUMANG = 108 NPTRA = 66 NATYP = 36 NPHB = 0 IFBOX = 0 NMXRS = 43 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 567848 | Hollerith 24165 | Integer 1061772 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 8678 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 -1.0841E+04 1.7186E+01 1.2605E+02 C 2349 BOND = 1379.1749 ANGLE = 3639.4818 DIHED = 5407.3565 VDWAALS = -3897.8925 EEL = -34910.3528 EGB = -7834.6657 1-4 VDW = 1789.3243 1-4 EEL = 23399.5518 RESTRAINT = 0.0000 ESURF = 186.7140 minimization completed, ENE= -.10841308E+05 RMS= 0.171857E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0821E+04 1.7261E+01 1.1016E+02 C 2393 BOND = 1408.0655 ANGLE = 3732.8162 DIHED = 5422.3838 VDWAALS = -3923.7571 EEL = -35073.7099 EGB = -7753.4168 1-4 VDW = 1799.9587 1-4 EEL = 23380.9345 RESTRAINT = 0.0000 ESURF = 185.7478 minimization completed, ENE= -.10820977E+05 RMS= 0.172615E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0799E+04 1.7007E+01 1.2870E+02 CA 5975 BOND = 1405.3705 ANGLE = 3718.4172 DIHED = 5420.3864 VDWAALS = -3879.7721 EEL = -34900.7472 EGB = -7817.6263 1-4 VDW = 1773.5644 1-4 EEL = 23294.5700 RESTRAINT = 0.0000 ESURF = 186.8959 minimization completed, ENE= -.10798941E+05 RMS= 0.170070E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0813E+04 1.7441E+01 1.2697E+02 C 7452 BOND = 1433.4037 ANGLE = 3639.4450 DIHED = 5412.3716 VDWAALS = -3884.3170 EEL = -35071.9043 EGB = -7669.8566 1-4 VDW = 1818.0545 1-4 EEL = 23325.1919 RESTRAINT = 0.0000 ESURF = 184.6957 minimization completed, ENE= -.10812916E+05 RMS= 0.174413E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0652E+04 1.7072E+01 1.1159E+02 C 6327 BOND = 1409.4251 ANGLE = 3735.8931 DIHED = 5463.7986 VDWAALS = -3888.9320 EEL = -35104.1961 EGB = -7573.1844 1-4 VDW = 1801.7800 1-4 EEL = 23319.2620 RESTRAINT = 0.0000 ESURF = 183.8065 minimization completed, ENE= -.10652347E+05 RMS= 0.170725E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0756E+04 1.7323E+01 1.2963E+02 C 3872 BOND = 1408.8741 ANGLE = 3685.1027 DIHED = 5450.4478 VDWAALS = -3897.3193 EEL = -35053.9178 EGB = -7638.8622 1-4 VDW = 1796.6272 1-4 EEL = 23308.3257 RESTRAINT = 0.0000 ESURF = 184.3686 minimization completed, ENE= -.10756353E+05 RMS= 0.173235E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0788E+04 1.7403E+01 1.1245E+02 C 113 BOND = 1404.7961 ANGLE = 3738.4015 DIHED = 5389.3866 VDWAALS = -3847.3428 EEL = -35042.6756 EGB = -7686.3880 1-4 VDW = 1768.2777 1-4 EEL = 23302.3115 RESTRAINT = 0.0000 ESURF = 185.2168 minimization completed, ENE= -.10788016E+05 RMS= 0.174031E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0828E+04 1.7223E+01 1.1445E+02 N 6201 BOND = 1440.5013 ANGLE = 3695.4152 DIHED = 5369.5071 VDWAALS = -3928.3274 EEL = -35119.9287 EGB = -7627.4828 1-4 VDW = 1773.3684 1-4 EEL = 23385.7240 RESTRAINT = 0.0000 ESURF = 183.6450 minimization completed, ENE= -.10827578E+05 RMS= 0.172229E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0826E+04 1.7224E+01 1.1347E+02 C 1454 BOND = 1379.6930 ANGLE = 3733.7302 DIHED = 5392.7060 VDWAALS = -3919.0988 EEL = -35021.9708 EGB = -7686.3757 1-4 VDW = 1771.4681 1-4 EEL = 23338.8527 RESTRAINT = 0.0000 ESURF = 184.5919 minimization completed, ENE= -.10826403E+05 RMS= 0.172236E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0707E+04 1.7459E+01 1.3614E+02 CG 5359 BOND = 1441.7883 ANGLE = 3694.2994 DIHED = 5458.2712 VDWAALS = -3926.6650 EEL = -35286.7281 EGB = -7493.8288 1-4 VDW = 1814.8575 1-4 EEL = 23408.1379 RESTRAINT = 0.0000 ESURF = 182.4668 minimization completed, ENE= -.10707401E+05 RMS= 0.174587E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0705E+04 1.7516E+01 1.3784E+02 C 2030 BOND = 1452.9252 ANGLE = 3796.1259 DIHED = 5443.5111 VDWAALS = -3913.5536 EEL = -35203.7591 EGB = -7545.4456 1-4 VDW = 1780.9350 1-4 EEL = 23300.2025 RESTRAINT = 0.0000 ESURF = 183.9734 minimization completed, ENE= -.10705085E+05 RMS= 0.175160E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0764E+04 1.7231E+01 1.1490E+02 C 5940 BOND = 1385.9658 ANGLE = 3756.1715 DIHED = 5431.0473 VDWAALS = -3871.9006 EEL = -35207.6097 EGB = -7526.8025 1-4 VDW = 1773.1879 1-4 EEL = 23310.1984 RESTRAINT = 0.0000 ESURF = 185.3618 minimization completed, ENE= -.10764380E+05 RMS= 0.172314E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0695E+04 1.7259E+01 1.0995E+02 C 1768 BOND = 1390.9207 ANGLE = 3787.9736 DIHED = 5420.1720 VDWAALS = -3868.0399 EEL = -35102.0397 EGB = -7593.9637 1-4 VDW = 1791.0846 1-4 EEL = 23293.4730 RESTRAINT = 0.0000 ESURF = 185.3314 minimization completed, ENE= -.10695088E+05 RMS= 0.172591E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0656E+04 1.7284E+01 1.0912E+02 C 884 BOND = 1424.3714 ANGLE = 3756.3475 DIHED = 5453.7396 VDWAALS = -3843.6732 EEL = -35149.7943 EGB = -7605.2178 1-4 VDW = 1777.8673 1-4 EEL = 23346.3862 RESTRAINT = 0.0000 ESURF = 184.1050 minimization completed, ENE= -.10655868E+05 RMS= 0.172837E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0812E+04 1.7242E+01 1.0299E+02 C 903 BOND = 1409.1453 ANGLE = 3660.7911 DIHED = 5451.3050 VDWAALS = -3870.2403 EEL = -34979.5144 EGB = -7809.7979 1-4 VDW = 1803.3042 1-4 EEL = 23336.7794 RESTRAINT = 0.0000 ESURF = 185.9881 minimization completed, ENE= -.10812239E+05 RMS= 0.172422E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0793E+04 1.7403E+01 1.0834E+02 CB 4254 BOND = 1433.0128 ANGLE = 3714.3642 DIHED = 5396.0868 VDWAALS = -3873.9129 EEL = -35109.1023 EGB = -7604.3867 1-4 VDW = 1776.5741 1-4 EEL = 23287.9001 RESTRAINT = 0.0000 ESURF = 186.4853 minimization completed, ENE= -.10792979E+05 RMS= 0.174026E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0813E+04 1.7219E+01 1.0380E+02 CG 1287 BOND = 1413.5772 ANGLE = 3704.4037 DIHED = 5396.5778 VDWAALS = -3895.5440 EEL = -35062.3968 EGB = -7612.8775 1-4 VDW = 1773.3230 1-4 EEL = 23284.8434 RESTRAINT = 0.0000 ESURF = 185.1039 minimization completed, ENE= -.10812989E+05 RMS= 0.172188E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0737E+04 1.7211E+01 1.2255E+02 CG 129 BOND = 1413.6557 ANGLE = 3781.6200 DIHED = 5434.1816 VDWAALS = -3905.4583 EEL = -35115.2535 EGB = -7625.1806 1-4 VDW = 1782.3180 1-4 EEL = 23313.1540 RESTRAINT = 0.0000 ESURF = 184.1248 minimization completed, ENE= -.10736838E+05 RMS= 0.172113E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0780E+04 1.7185E+01 1.1684E+02 C 7741 BOND = 1414.8945 ANGLE = 3678.2863 DIHED = 5412.2667 VDWAALS = -3847.5169 EEL = -35247.6834 EGB = -7575.8507 1-4 VDW = 1812.0085 1-4 EEL = 23387.1083 RESTRAINT = 0.0000 ESURF = 186.1908 minimization completed, ENE= -.10780296E+05 RMS= 0.171853E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0611E+04 1.7432E+01 1.3510E+02 CG 3206 BOND = 1439.4708 ANGLE = 3763.5885 DIHED = 5440.7114 VDWAALS = -3878.4156 EEL = -34892.8812 EGB = -7779.9308 1-4 VDW = 1794.5524 1-4 EEL = 23311.7112 RESTRAINT = 0.0000 ESURF = 189.7290 minimization completed, ENE= -.10611464E+05 RMS= 0.174324E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0620E+04 1.7506E+01 1.2467E+02 C 7547 BOND = 1447.1608 ANGLE = 3755.9654 DIHED = 5424.6590 VDWAALS = -3902.9093 EEL = -34949.7448 EGB = -7728.3241 1-4 VDW = 1822.6803 1-4 EEL = 23322.9747 RESTRAINT = 0.0000 ESURF = 187.4177 minimization completed, ENE= -.10620120E+05 RMS= 0.175063E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0644E+04 1.7520E+01 1.0810E+02 CA 1265 BOND = 1431.7065 ANGLE = 3758.4987 DIHED = 5474.0720 VDWAALS = -3908.5321 EEL = -35054.5999 EGB = -7659.7957 1-4 VDW = 1796.7902 1-4 EEL = 23330.0725 RESTRAINT = 0.0000 ESURF = 187.8609 minimization completed, ENE= -.10643927E+05 RMS= 0.175203E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0675E+04 1.7407E+01 1.0185E+02 C 6782 BOND = 1436.1278 ANGLE = 3712.1795 DIHED = 5455.1385 VDWAALS = -3930.6000 EEL = -34857.2306 EGB = -7780.6252 1-4 VDW = 1781.1961 1-4 EEL = 23321.0588 RESTRAINT = 0.0000 ESURF = 187.5075 minimization completed, ENE= -.10675248E+05 RMS= 0.174073E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0759E+04 1.7215E+01 1.1758E+02 C 2308 BOND = 1436.5282 ANGLE = 3668.7007 DIHED = 5377.3951 VDWAALS = -3898.3595 EEL = -34795.4199 EGB = -7907.2488 1-4 VDW = 1828.0368 1-4 EEL = 23342.6010 RESTRAINT = 0.0000 ESURF = 189.2520 minimization completed, ENE= -.10758514E+05 RMS= 0.172147E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0659E+04 1.7198E+01 9.7333E+01 CD 2390 BOND = 1409.5432 ANGLE = 3794.9456 DIHED = 5423.1509 VDWAALS = -3885.6797 EEL = -34749.6718 EGB = -7999.8227 1-4 VDW = 1788.0860 1-4 EEL = 23371.9622 RESTRAINT = 0.0000 ESURF = 188.6547 minimization completed, ENE= -.10658832E+05 RMS= 0.171978E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0788E+04 1.7307E+01 1.1110E+02 C 2951 BOND = 1377.4518 ANGLE = 3685.0142 DIHED = 5407.7594 VDWAALS = -3910.8217 EEL = -35011.1355 EGB = -7804.1586 1-4 VDW = 1849.8417 1-4 EEL = 23429.9196 RESTRAINT = 0.0000 ESURF = 188.0356 minimization completed, ENE= -.10788094E+05 RMS= 0.173068E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0716E+04 1.7183E+01 9.6216E+01 N 4163 BOND = 1459.4327 ANGLE = 3708.9897 DIHED = 5442.8488 VDWAALS = -3903.0624 EEL = -34936.8132 EGB = -7851.4072 1-4 VDW = 1795.1017 1-4 EEL = 23380.2355 RESTRAINT = 0.0000 ESURF = 188.8451 minimization completed, ENE= -.10715829E+05 RMS= 0.171826E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0735E+04 1.7308E+01 1.1639E+02 CG 3132 BOND = 1390.9040 ANGLE = 3797.4890 DIHED = 5411.6066 VDWAALS = -3876.6416 EEL = -35088.8984 EGB = -7737.1768 1-4 VDW = 1770.2335 1-4 EEL = 23408.4975 RESTRAINT = 0.0000 ESURF = 188.5880 minimization completed, ENE= -.10735398E+05 RMS= 0.173083E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0727E+04 1.7301E+01 1.1023E+02 C 3427 BOND = 1423.0137 ANGLE = 3736.0722 DIHED = 5379.0154 VDWAALS = -3904.6064 EEL = -34984.5322 EGB = -7777.0480 1-4 VDW = 1804.6541 1-4 EEL = 23408.3548 RESTRAINT = 0.0000 ESURF = 188.2961 minimization completed, ENE= -.10726780E+05 RMS= 0.173015E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0708E+04 1.7256E+01 1.1269E+02 N 287 BOND = 1426.7659 ANGLE = 3693.7255 DIHED = 5443.7622 VDWAALS = -3839.7533 EEL = -35174.7290 EGB = -7623.1698 1-4 VDW = 1806.5140 1-4 EEL = 23369.9835 RESTRAINT = 0.0000 ESURF = 188.6141 minimization completed, ENE= -.10708287E+05 RMS= 0.172562E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0671E+04 1.7575E+01 1.1407E+02 C 7588 BOND = 1424.5553 ANGLE = 3859.7777 DIHED = 5440.0456 VDWAALS = -3935.5374 EEL = -35186.3484 EGB = -7622.3387 1-4 VDW = 1803.7810 1-4 EEL = 23359.2508 RESTRAINT = 0.0000 ESURF = 186.0686 minimization completed, ENE= -.10670745E+05 RMS= 0.175748E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0731E+04 1.7313E+01 1.2191E+02 C 6389 BOND = 1397.9123 ANGLE = 3705.6657 DIHED = 5459.5813 VDWAALS = -3896.9098 EEL = -35175.1945 EGB = -7632.4131 1-4 VDW = 1811.4645 1-4 EEL = 23411.3273 RESTRAINT = 0.0000 ESURF = 187.0763 minimization completed, ENE= -.10731490E+05 RMS= 0.173131E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0737E+04 1.7148E+01 1.2394E+02 CG 4706 BOND = 1452.8056 ANGLE = 3734.1396 DIHED = 5441.0570 VDWAALS = -3891.7492 EEL = -35012.4578 EGB = -7774.7914 1-4 VDW = 1767.0190 1-4 EEL = 23360.2191 RESTRAINT = 0.0000 ESURF = 187.0100 minimization completed, ENE= -.10736748E+05 RMS= 0.171480E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0776E+04 1.7284E+01 1.0941E+02 C 5598 BOND = 1436.4209 ANGLE = 3729.1805 DIHED = 5453.5518 VDWAALS = -3890.8869 EEL = -35122.3470 EGB = -7680.5122 1-4 VDW = 1807.5436 1-4 EEL = 23304.1051 RESTRAINT = 0.0000 ESURF = 186.6744 minimization completed, ENE= -.10776270E+05 RMS= 0.172840E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0755E+04 1.7357E+01 1.0910E+02 C 2514 BOND = 1441.5114 ANGLE = 3711.2485 DIHED = 5445.1397 VDWAALS = -3865.4065 EEL = -35002.7512 EGB = -7779.3177 1-4 VDW = 1773.7505 1-4 EEL = 23330.4090 RESTRAINT = 0.0000 ESURF = 189.9981 minimization completed, ENE= -.10755418E+05 RMS= 0.173567E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0680E+04 1.7367E+01 1.2944E+02 CG 5359 BOND = 1418.4109 ANGLE = 3761.9547 DIHED = 5404.5521 VDWAALS = -3823.0026 EEL = -34989.4290 EGB = -7803.3794 1-4 VDW = 1808.5724 1-4 EEL = 23352.7213 RESTRAINT = 0.0000 ESURF = 189.9588 minimization completed, ENE= -.10679641E+05 RMS= 0.173668E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0759E+04 1.7220E+01 1.1288E+02 C 2125 BOND = 1396.4370 ANGLE = 3746.7909 DIHED = 5419.6223 VDWAALS = -3908.8318 EEL = -34905.7263 EGB = -7889.8831 1-4 VDW = 1805.8471 1-4 EEL = 23389.3076 RESTRAINT = 0.0000 ESURF = 187.1206 minimization completed, ENE= -.10759316E+05 RMS= 0.172204E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0708E+04 1.7432E+01 1.1033E+02 C 2537 BOND = 1449.0749 ANGLE = 3762.7932 DIHED = 5440.1985 VDWAALS = -3926.2856 EEL = -34828.6474 EGB = -7904.2755 1-4 VDW = 1781.0184 1-4 EEL = 23331.0135 RESTRAINT = 0.0000 ESURF = 186.9767 minimization completed, ENE= -.10708133E+05 RMS= 0.174324E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0754E+04 1.7396E+01 1.2164E+02 C 1742 BOND = 1440.1983 ANGLE = 3754.6481 DIHED = 5389.5411 VDWAALS = -3817.7190 EEL = -34957.0045 EGB = -7862.4415 1-4 VDW = 1796.0919 1-4 EEL = 23314.0397 RESTRAINT = 0.0000 ESURF = 188.9001 minimization completed, ENE= -.10753746E+05 RMS= 0.173963E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0761E+04 1.7350E+01 1.3770E+02 CZ 4217 BOND = 1426.9627 ANGLE = 3643.7719 DIHED = 5423.4499 VDWAALS = -3845.0593 EEL = -34798.7473 EGB = -7960.8747 1-4 VDW = 1795.4730 1-4 EEL = 23365.8830 RESTRAINT = 0.0000 ESURF = 188.5192 minimization completed, ENE= -.10760622E+05 RMS= 0.173500E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0708E+04 1.7416E+01 1.1022E+02 CD 2779 BOND = 1456.8481 ANGLE = 3770.0912 DIHED = 5397.8134 VDWAALS = -3848.6575 EEL = -34790.6371 EGB = -7968.6093 1-4 VDW = 1781.7401 1-4 EEL = 23304.9477 RESTRAINT = 0.0000 ESURF = 188.5154 minimization completed, ENE= -.10707948E+05 RMS= 0.174158E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0783E+04 1.7361E+01 1.1123E+02 C 120 BOND = 1389.4648 ANGLE = 3724.3099 DIHED = 5386.8735 VDWAALS = -3849.9052 EEL = -34897.0885 EGB = -7847.5476 1-4 VDW = 1788.5073 1-4 EEL = 23334.0417 RESTRAINT = 0.0000 ESURF = 188.5573 minimization completed, ENE= -.10782787E+05 RMS= 0.173606E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0804E+04 1.7194E+01 1.0879E+02 CA 5083 BOND = 1381.1709 ANGLE = 3775.7586 DIHED = 5391.2255 VDWAALS = -3927.1910 EEL = -34907.4309 EGB = -7859.3795 1-4 VDW = 1777.8336 1-4 EEL = 23377.3503 RESTRAINT = 0.0000 ESURF = 187.0120 minimization completed, ENE= -.10803651E+05 RMS= 0.171935E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0882E+04 1.7236E+01 1.0919E+02 C 6468 BOND = 1381.4460 ANGLE = 3719.3771 DIHED = 5393.1975 VDWAALS = -3889.0534 EEL = -35131.3355 EGB = -7767.3915 1-4 VDW = 1811.1181 1-4 EEL = 23413.8807 RESTRAINT = 0.0000 ESURF = 187.0927 minimization completed, ENE= -.10881668E+05 RMS= 0.172364E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0621E+04 1.7529E+01 1.0896E+02 C 2634 BOND = 1418.1598 ANGLE = 3854.9424 DIHED = 5420.4653 VDWAALS = -3913.7721 EEL = -34973.8679 EGB = -7714.3538 1-4 VDW = 1797.1510 1-4 EEL = 23303.2070 RESTRAINT = 0.0000 ESURF = 186.8888 minimization completed, ENE= -.10621180E+05 RMS= 0.175289E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0623E+04 1.7452E+01 1.2283E+02 C 964 BOND = 1426.3425 ANGLE = 3755.3637 DIHED = 5419.7984 VDWAALS = -3847.1423 EEL = -34925.9753 EGB = -7806.5546 1-4 VDW = 1812.2566 1-4 EEL = 23355.9293 RESTRAINT = 0.0000 ESURF = 186.9311 minimization completed, ENE= -.10623050E+05 RMS= 0.174516E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0728E+04 1.7292E+01 1.2342E+02 C 5395 BOND = 1407.4917 ANGLE = 3780.3081 DIHED = 5415.5297 VDWAALS = -3911.0045 EEL = -34998.7990 EGB = -7816.2593 1-4 VDW = 1799.9791 1-4 EEL = 23408.3174 RESTRAINT = 0.0000 ESURF = 186.7787 minimization completed, ENE= -.10727658E+05 RMS= 0.172921E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0614E+04 1.7438E+01 1.1561E+02 N 7194 BOND = 1422.5745 ANGLE = 3905.0857 DIHED = 5475.7732 VDWAALS = -3902.2144 EEL = -34885.9706 EGB = -7858.9785 1-4 VDW = 1781.9406 1-4 EEL = 23262.0230 RESTRAINT = 0.0000 ESURF = 185.3585 minimization completed, ENE= -.10614408E+05 RMS= 0.174382E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0726E+04 1.7403E+01 1.1411E+02 C 3427 BOND = 1435.3179 ANGLE = 3717.2324 DIHED = 5425.2404 VDWAALS = -3848.1395 EEL = -34960.9487 EGB = -7780.8786 1-4 VDW = 1780.2581 1-4 EEL = 23318.2987 RESTRAINT = 0.0000 ESURF = 187.6065 minimization completed, ENE= -.10726013E+05 RMS= 0.174025E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0704E+04 1.7318E+01 1.0550E+02 C 278 BOND = 1414.6810 ANGLE = 3787.6046 DIHED = 5426.9490 VDWAALS = -3879.6439 EEL = -34981.3249 EGB = -7797.5662 1-4 VDW = 1807.5650 1-4 EEL = 23330.6719 RESTRAINT = 0.0000 ESURF = 186.7076 minimization completed, ENE= -.10704356E+05 RMS= 0.173177E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 661.90 ( 7.37% of Gen B) | Calc gb diag 5350.54 (59.58% of Gen B) | Calc gb off-diag 2968.71 (33.05% of Gen B) | Gen Born time 8981.15 (100.0% of Nonbo) | Nonbond force 8981.15 (100.0% of Force) | Bond/Angle/Dihedral 5.36 ( 0.06% of Force) | Force time 8986.52 (100.0% of Runmd) | Runmd Time 8986.52 (98.99% of Total) | Other 91.70 ( 1.01% of Total) | Total time 9078.24 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 00:30:17.323 on 10/20/2010 | Setup done at 00:30:20.356 on 10/20/2010 | Run done at 03:01:35.561 on 10/20/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/20/2010 at 00:30:17 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _lig.out.9 |INPCRD: 1XCK_chainA_MGATP_noWAT.inpcrd | PARM: 1XCK_chainA_MGATP_noWAT.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _lig.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 = 09/24/09 Time = 02:43:23 NATOM = 7879 NTYPES = 18 NBONH = 3991 MBONA = 3917 NTHETH = 9115 MTHETA = 5297 NPHIH = 17023 MPHIA = 12427 NHPARM = 0 NPARM = 0 NNB = 43422 NRES = 526 NBONA = 3917 NTHETA = 5297 NPHIA = 12427 NUMBND = 52 NUMANG = 108 NPTRA = 66 NATYP = 36 NPHB = 0 IFBOX = 0 NMXRS = 43 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 567848 | Hollerith 24165 | Integer 1061772 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 8678 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 -1.0693E+04 1.7470E+01 1.3063E+02 CD 4694 BOND = 1397.4755 ANGLE = 3754.6716 DIHED = 5444.4881 VDWAALS = -3920.9491 EEL = -34929.5689 EGB = -7785.1074 1-4 VDW = 1819.1562 1-4 EEL = 23337.3916 RESTRAINT = 0.0000 ESURF = 189.6065 minimization completed, ENE= -.10692836E+05 RMS= 0.174695E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0675E+04 1.7268E+01 1.1403E+02 C 6360 BOND = 1418.1423 ANGLE = 3754.7006 DIHED = 5429.3160 VDWAALS = -3865.5023 EEL = -34857.0910 EGB = -7813.8427 1-4 VDW = 1829.8690 1-4 EEL = 23241.9008 RESTRAINT = 0.0000 ESURF = 187.9922 minimization completed, ENE= -.10674515E+05 RMS= 0.172676E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0696E+04 1.7333E+01 1.1188E+02 N 1929 BOND = 1431.5271 ANGLE = 3708.9333 DIHED = 5392.2720 VDWAALS = -3868.3554 EEL = -34797.7137 EGB = -7885.2054 1-4 VDW = 1834.1725 1-4 EEL = 23300.1299 RESTRAINT = 0.0000 ESURF = 188.4015 minimization completed, ENE= -.10695838E+05 RMS= 0.173325E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0736E+04 1.7324E+01 1.0559E+02 C 1812 BOND = 1407.6018 ANGLE = 3728.3703 DIHED = 5402.2389 VDWAALS = -3885.9031 EEL = -34885.3062 EGB = -7832.4918 1-4 VDW = 1799.3657 1-4 EEL = 23342.6781 RESTRAINT = 0.0000 ESURF = 187.5674 minimization completed, ENE= -.10735879E+05 RMS= 0.173236E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0698E+04 1.7389E+01 1.1810E+02 C 6301 BOND = 1462.3146 ANGLE = 3710.5775 DIHED = 5443.1854 VDWAALS = -3878.8506 EEL = -35033.6165 EGB = -7756.0999 1-4 VDW = 1825.1336 1-4 EEL = 23342.1594 RESTRAINT = 0.0000 ESURF = 187.6446 minimization completed, ENE= -.10697552E+05 RMS= 0.173885E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0695E+04 1.7623E+01 1.1321E+02 C 93 BOND = 1464.0239 ANGLE = 3754.8135 DIHED = 5370.5343 VDWAALS = -3868.3671 EEL = -35029.1168 EGB = -7813.0407 1-4 VDW = 1812.9616 1-4 EEL = 23426.0594 RESTRAINT = 0.0000 ESURF = 186.9638 minimization completed, ENE= -.10695168E+05 RMS= 0.176231E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0670E+04 1.7287E+01 1.0553E+02 C 7819 BOND = 1402.5629 ANGLE = 3782.2816 DIHED = 5472.5003 VDWAALS = -3915.8747 EEL = -34826.8130 EGB = -7826.0972 1-4 VDW = 1782.4944 1-4 EEL = 23271.2932 RESTRAINT = 0.0000 ESURF = 188.1376 minimization completed, ENE= -.10669515E+05 RMS= 0.172870E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0757E+04 1.7273E+01 1.4623E+02 PA 7846 BOND = 1381.1415 ANGLE = 3763.0152 DIHED = 5438.7651 VDWAALS = -3920.4290 EEL = -34877.6671 EGB = -7848.2267 1-4 VDW = 1797.6450 1-4 EEL = 23322.0520 RESTRAINT = 0.0000 ESURF = 187.0086 minimization completed, ENE= -.10756695E+05 RMS= 0.172734E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0707E+04 1.7407E+01 1.2422E+02 CD 3539 BOND = 1407.2917 ANGLE = 3738.8814 DIHED = 5423.1784 VDWAALS = -3883.6423 EEL = -35006.3139 EGB = -7738.5780 1-4 VDW = 1836.4959 1-4 EEL = 23330.0514 RESTRAINT = 0.0000 ESURF = 185.9841 minimization completed, ENE= -.10706651E+05 RMS= 0.174069E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0729E+04 1.7360E+01 1.2451E+02 CD 3439 BOND = 1441.5521 ANGLE = 3737.1467 DIHED = 5406.7953 VDWAALS = -3867.6652 EEL = -34980.0550 EGB = -7735.3824 1-4 VDW = 1769.8604 1-4 EEL = 23310.9997 RESTRAINT = 0.0000 ESURF = 187.4739 minimization completed, ENE= -.10729274E+05 RMS= 0.173601E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0735E+04 1.7403E+01 1.2310E+02 CG 2228 BOND = 1446.7415 ANGLE = 3753.5443 DIHED = 5397.2114 VDWAALS = -3930.9468 EEL = -35020.6899 EGB = -7667.7556 1-4 VDW = 1802.2280 1-4 EEL = 23297.9649 RESTRAINT = 0.0000 ESURF = 186.5746 minimization completed, ENE= -.10735128E+05 RMS= 0.174028E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0759E+04 1.7380E+01 1.2317E+02 CA 289 BOND = 1423.5351 ANGLE = 3743.0634 DIHED = 5421.6364 VDWAALS = -3906.4401 EEL = -35004.9882 EGB = -7728.5177 1-4 VDW = 1764.4931 1-4 EEL = 23342.6517 RESTRAINT = 0.0000 ESURF = 185.2620 minimization completed, ENE= -.10759304E+05 RMS= 0.173796E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0701E+04 1.7319E+01 1.0948E+02 CG 3293 BOND = 1411.8085 ANGLE = 3755.2970 DIHED = 5432.6902 VDWAALS = -3891.5646 EEL = -34993.7530 EGB = -7676.4328 1-4 VDW = 1793.3884 1-4 EEL = 23281.1153 RESTRAINT = 0.0000 ESURF = 186.5118 minimization completed, ENE= -.10700939E+05 RMS= 0.173190E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0751E+04 1.7150E+01 1.1490E+02 C 3610 BOND = 1395.3960 ANGLE = 3708.5029 DIHED = 5438.5383 VDWAALS = -3852.2874 EEL = -34996.6117 EGB = -7765.7920 1-4 VDW = 1809.9498 1-4 EEL = 23324.3747 RESTRAINT = 0.0000 ESURF = 186.7638 minimization completed, ENE= -.10751166E+05 RMS= 0.171503E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0622E+04 1.7563E+01 1.1622E+02 C 4161 BOND = 1454.5109 ANGLE = 3781.1723 DIHED = 5441.0332 VDWAALS = -3932.9733 EEL = -35077.6189 EGB = -7594.7105 1-4 VDW = 1815.4699 1-4 EEL = 23305.5993 RESTRAINT = 0.0000 ESURF = 185.4760 minimization completed, ENE= -.10622041E+05 RMS= 0.175632E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0675E+04 1.7302E+01 1.1438E+02 C 4188 BOND = 1415.5643 ANGLE = 3720.1020 DIHED = 5426.6340 VDWAALS = -3899.0407 EEL = -35010.0793 EGB = -7685.3758 1-4 VDW = 1833.7019 1-4 EEL = 23341.3265 RESTRAINT = 0.0000 ESURF = 182.6483 minimization completed, ENE= -.10674519E+05 RMS= 0.173022E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0698E+04 1.7279E+01 1.1229E+02 CD 4522 BOND = 1411.4869 ANGLE = 3722.9193 DIHED = 5422.7343 VDWAALS = -3902.0354 EEL = -34878.6388 EGB = -7783.2859 1-4 VDW = 1814.1800 1-4 EEL = 23309.0168 RESTRAINT = 0.0000 ESURF = 185.6428 minimization completed, ENE= -.10697980E+05 RMS= 0.172787E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0681E+04 1.7433E+01 1.0611E+02 C 835 BOND = 1462.8594 ANGLE = 3731.7023 DIHED = 5444.1044 VDWAALS = -3916.9663 EEL = -34989.4936 EGB = -7750.8668 1-4 VDW = 1792.6119 1-4 EEL = 23358.5795 RESTRAINT = 0.0000 ESURF = 186.3645 minimization completed, ENE= -.10681105E+05 RMS= 0.174334E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0721E+04 1.7565E+01 1.3135E+02 CD 6794 BOND = 1433.4101 ANGLE = 3722.4014 DIHED = 5420.0228 VDWAALS = -3914.1933 EEL = -34875.8868 EGB = -7792.6707 1-4 VDW = 1788.7630 1-4 EEL = 23310.1546 RESTRAINT = 0.0000 ESURF = 186.7674 minimization completed, ENE= -.10721231E+05 RMS= 0.175647E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0666E+04 1.7429E+01 1.3089E+02 CD 4747 BOND = 1405.6241 ANGLE = 3800.0329 DIHED = 5413.0723 VDWAALS = -3914.3349 EEL = -34787.4879 EGB = -7808.3731 1-4 VDW = 1803.8503 1-4 EEL = 23234.9917 RESTRAINT = 0.0000 ESURF = 187.0597 minimization completed, ENE= -.10665565E+05 RMS= 0.174288E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0639E+04 1.7498E+01 1.2741E+02 C 3284 BOND = 1444.0507 ANGLE = 3763.8870 DIHED = 5421.2406 VDWAALS = -3923.0470 EEL = -34975.8504 EGB = -7715.1749 1-4 VDW = 1813.2439 1-4 EEL = 23348.7169 RESTRAINT = 0.0000 ESURF = 184.0504 minimization completed, ENE= -.10638883E+05 RMS= 0.174976E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0774E+04 1.7291E+01 1.3718E+02 N 559 BOND = 1414.4415 ANGLE = 3752.2512 DIHED = 5410.3935 VDWAALS = -3937.7094 EEL = -34973.5294 EGB = -7790.1878 1-4 VDW = 1792.2072 1-4 EEL = 23373.3754 RESTRAINT = 0.0000 ESURF = 184.6893 minimization completed, ENE= -.10774068E+05 RMS= 0.172907E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0688E+04 1.7436E+01 1.1016E+02 N 2021 BOND = 1445.9224 ANGLE = 3721.9737 DIHED = 5449.9237 VDWAALS = -3867.2569 EEL = -35000.2398 EGB = -7742.4976 1-4 VDW = 1821.0733 1-4 EEL = 23297.4746 RESTRAINT = 0.0000 ESURF = 186.0299 minimization completed, ENE= -.10687597E+05 RMS= 0.174358E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0713E+04 1.7188E+01 1.2365E+02 C 1852 BOND = 1401.3728 ANGLE = 3748.4725 DIHED = 5448.7017 VDWAALS = -3940.2251 EEL = -34683.9671 EGB = -8057.8275 1-4 VDW = 1802.9373 1-4 EEL = 23381.4698 RESTRAINT = 0.0000 ESURF = 186.2532 minimization completed, ENE= -.10712812E+05 RMS= 0.171884E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0823E+04 1.7021E+01 1.1019E+02 CD 5041 BOND = 1355.9800 ANGLE = 3739.2695 DIHED = 5447.1881 VDWAALS = -3936.7505 EEL = -34900.6211 EGB = -7816.9068 1-4 VDW = 1784.8371 1-4 EEL = 23316.9224 RESTRAINT = 0.0000 ESURF = 187.1117 minimization completed, ENE= -.10822969E+05 RMS= 0.170210E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0762E+04 1.7274E+01 1.2595E+02 CZ 5933 BOND = 1355.2738 ANGLE = 3703.2030 DIHED = 5424.5718 VDWAALS = -3891.2937 EEL = -35058.8061 EGB = -7751.7391 1-4 VDW = 1851.4008 1-4 EEL = 23418.5418 RESTRAINT = 0.0000 ESURF = 186.3829 minimization completed, ENE= -.10762465E+05 RMS= 0.172738E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0633E+04 1.7338E+01 1.0735E+02 CE 36 BOND = 1420.2545 ANGLE = 3783.9841 DIHED = 5454.5737 VDWAALS = -3877.9160 EEL = -34892.0757 EGB = -7875.7561 1-4 VDW = 1798.7785 1-4 EEL = 23368.2578 RESTRAINT = 0.0000 ESURF = 187.2743 minimization completed, ENE= -.10632625E+05 RMS= 0.173383E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0840E+04 1.7194E+01 1.0721E+02 CG 2895 BOND = 1425.2307 ANGLE = 3648.9475 DIHED = 5420.2925 VDWAALS = -3907.2904 EEL = -34804.0524 EGB = -7943.0818 1-4 VDW = 1812.0966 1-4 EEL = 23321.5853 RESTRAINT = 0.0000 ESURF = 186.2494 minimization completed, ENE= -.10840023E+05 RMS= 0.171937E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0615E+04 1.7519E+01 1.3130E+02 CD 5504 BOND = 1479.5817 ANGLE = 3754.6790 DIHED = 5450.7128 VDWAALS = -3881.5580 EEL = -34777.3234 EGB = -7921.8516 1-4 VDW = 1808.6267 1-4 EEL = 23284.6072 RESTRAINT = 0.0000 ESURF = 187.3543 minimization completed, ENE= -.10615171E+05 RMS= 0.175194E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0702E+04 1.7241E+01 1.0889E+02 C 704 BOND = 1408.4348 ANGLE = 3728.6290 DIHED = 5439.7607 VDWAALS = -3876.1725 EEL = -34751.0386 EGB = -7918.0863 1-4 VDW = 1808.7343 1-4 EEL = 23271.8273 RESTRAINT = 0.0000 ESURF = 186.3540 minimization completed, ENE= -.10701557E+05 RMS= 0.172406E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0598E+04 1.7425E+01 1.0849E+02 CD 3794 BOND = 1437.5925 ANGLE = 3794.8185 DIHED = 5412.6559 VDWAALS = -3903.2105 EEL = -34720.1133 EGB = -7957.1273 1-4 VDW = 1826.1345 1-4 EEL = 23324.0282 RESTRAINT = 0.0000 ESURF = 187.6933 minimization completed, ENE= -.10597528E+05 RMS= 0.174254E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0686E+04 1.7264E+01 1.2467E+02 C 964 BOND = 1445.5839 ANGLE = 3741.5757 DIHED = 5408.5929 VDWAALS = -3893.9493 EEL = -34776.0361 EGB = -7906.6776 1-4 VDW = 1826.6845 1-4 EEL = 23279.8003 RESTRAINT = 0.0000 ESURF = 188.0167 minimization completed, ENE= -.10686409E+05 RMS= 0.172638E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0643E+04 1.7490E+01 1.1866E+02 CZ 6666 BOND = 1453.7982 ANGLE = 3716.1252 DIHED = 5451.8975 VDWAALS = -3825.5675 EEL = -34820.9249 EGB = -7871.1423 1-4 VDW = 1797.6386 1-4 EEL = 23266.3272 RESTRAINT = 0.0000 ESURF = 188.7641 minimization completed, ENE= -.10643084E+05 RMS= 0.174905E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0712E+04 1.7267E+01 1.1727E+02 N 5918 BOND = 1385.2075 ANGLE = 3763.1960 DIHED = 5457.6038 VDWAALS = -3873.5618 EEL = -34892.4214 EGB = -7840.2470 1-4 VDW = 1791.3908 1-4 EEL = 23309.2994 RESTRAINT = 0.0000 ESURF = 187.5128 minimization completed, ENE= -.10712020E+05 RMS= 0.172670E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0848E+04 1.7273E+01 1.1633E+02 C 4663 BOND = 1389.3851 ANGLE = 3672.9079 DIHED = 5434.3955 VDWAALS = -3871.9422 EEL = -34875.2528 EGB = -7905.9975 1-4 VDW = 1808.3377 1-4 EEL = 23309.3918 RESTRAINT = 0.0000 ESURF = 190.2756 minimization completed, ENE= -.10848499E+05 RMS= 0.172730E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0668E+04 1.7472E+01 1.0713E+02 CD 5041 BOND = 1436.0024 ANGLE = 3765.1895 DIHED = 5421.6026 VDWAALS = -3872.1998 EEL = -34820.6941 EGB = -7953.5795 1-4 VDW = 1819.2452 1-4 EEL = 23347.9857 RESTRAINT = 0.0000 ESURF = 188.9199 minimization completed, ENE= -.10667528E+05 RMS= 0.174717E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0595E+04 1.7210E+01 1.0700E+02 CA 7534 BOND = 1422.1546 ANGLE = 3750.5476 DIHED = 5442.3885 VDWAALS = -3856.4690 EEL = -34663.2579 EGB = -8061.3028 1-4 VDW = 1789.3354 1-4 EEL = 23391.9937 RESTRAINT = 0.0000 ESURF = 189.8450 minimization completed, ENE= -.10594765E+05 RMS= 0.172103E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0626E+04 1.7476E+01 1.2568E+02 CD 5041 BOND = 1432.4909 ANGLE = 3744.7019 DIHED = 5452.3408 VDWAALS = -3883.6636 EEL = -34667.1438 EGB = -8043.7540 1-4 VDW = 1818.8404 1-4 EEL = 23332.9632 RESTRAINT = 0.0000 ESURF = 186.9515 minimization completed, ENE= -.10626273E+05 RMS= 0.174757E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0779E+04 1.7367E+01 1.2261E+02 C 2537 BOND = 1426.3165 ANGLE = 3739.0903 DIHED = 5430.5920 VDWAALS = -3911.2809 EEL = -34656.3913 EGB = -8081.3894 1-4 VDW = 1760.5005 1-4 EEL = 23324.7253 RESTRAINT = 0.0000 ESURF = 189.2022 minimization completed, ENE= -.10778635E+05 RMS= 0.173665E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0702E+04 1.7094E+01 1.2078E+02 N 1511 BOND = 1377.5313 ANGLE = 3698.9606 DIHED = 5413.8369 VDWAALS = -3873.7987 EEL = -34767.8507 EGB = -7967.0101 1-4 VDW = 1864.7554 1-4 EEL = 23362.2842 RESTRAINT = 0.0000 ESURF = 189.2973 minimization completed, ENE= -.10701994E+05 RMS= 0.170938E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0668E+04 1.7159E+01 1.0562E+02 C 5146 BOND = 1377.1292 ANGLE = 3807.3578 DIHED = 5403.3794 VDWAALS = -3873.2831 EEL = -34735.5212 EGB = -7980.4575 1-4 VDW = 1791.8781 1-4 EEL = 23352.5241 RESTRAINT = 0.0000 ESURF = 189.0262 minimization completed, ENE= -.10667967E+05 RMS= 0.171591E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0693E+04 1.7419E+01 1.1162E+02 C 4873 BOND = 1342.2747 ANGLE = 3856.0587 DIHED = 5421.7662 VDWAALS = -3859.3426 EEL = -34829.8591 EGB = -7991.1983 1-4 VDW = 1830.6547 1-4 EEL = 23346.6367 RESTRAINT = 0.0000 ESURF = 189.7781 minimization completed, ENE= -.10693231E+05 RMS= 0.174190E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0593E+04 1.7554E+01 1.0529E+02 CA 3322 BOND = 1454.5515 ANGLE = 3843.0391 DIHED = 5396.6977 VDWAALS = -3866.4697 EEL = -34805.2411 EGB = -7873.7718 1-4 VDW = 1781.9412 1-4 EEL = 23286.1707 RESTRAINT = 0.0000 ESURF = 190.4000 minimization completed, ENE= -.10592683E+05 RMS= 0.175541E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0673E+04 1.7471E+01 1.3584E+02 CD 3135 BOND = 1467.1748 ANGLE = 3786.1068 DIHED = 5373.4997 VDWAALS = -3859.7469 EEL = -34890.9154 EGB = -7950.1131 1-4 VDW = 1807.4848 1-4 EEL = 23404.6780 RESTRAINT = 0.0000 ESURF = 189.1625 minimization completed, ENE= -.10672669E+05 RMS= 0.174706E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0624E+04 1.7447E+01 1.0123E+02 CA 2590 BOND = 1454.6880 ANGLE = 3783.9709 DIHED = 5407.6390 VDWAALS = -3879.7529 EEL = -34628.7710 EGB = -8029.4284 1-4 VDW = 1783.5066 1-4 EEL = 23295.4555 RESTRAINT = 0.0000 ESURF = 188.5696 minimization completed, ENE= -.10624123E+05 RMS= 0.174471E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0700E+04 1.7469E+01 1.0660E+02 C 7578 BOND = 1441.5797 ANGLE = 3711.4557 DIHED = 5434.5209 VDWAALS = -3909.6662 EEL = -34837.1045 EGB = -7879.3727 1-4 VDW = 1795.9983 1-4 EEL = 23353.9789 RESTRAINT = 0.0000 ESURF = 188.7375 minimization completed, ENE= -.10699872E+05 RMS= 0.174689E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0763E+04 1.7254E+01 1.1593E+02 CD 5041 BOND = 1403.8253 ANGLE = 3735.4624 DIHED = 5441.9790 VDWAALS = -3892.6057 EEL = -34714.9101 EGB = -8002.4993 1-4 VDW = 1782.0184 1-4 EEL = 23294.5829 RESTRAINT = 0.0000 ESURF = 188.9498 minimization completed, ENE= -.10763197E+05 RMS= 0.172540E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0695E+04 1.7498E+01 1.1108E+02 C 6940 BOND = 1414.1223 ANGLE = 3735.7519 DIHED = 5409.8382 VDWAALS = -3873.0046 EEL = -34837.0308 EGB = -7928.2735 1-4 VDW = 1789.6477 1-4 EEL = 23404.9749 RESTRAINT = 0.0000 ESURF = 189.1098 minimization completed, ENE= -.10694864E+05 RMS= 0.174983E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0785E+04 1.7274E+01 1.2346E+02 CB 710 BOND = 1419.7146 ANGLE = 3745.4312 DIHED = 5415.0064 VDWAALS = -3926.8672 EEL = -34777.3184 EGB = -7951.0968 1-4 VDW = 1763.8982 1-4 EEL = 23336.9446 RESTRAINT = 0.0000 ESURF = 188.9053 minimization completed, ENE= -.10785382E+05 RMS= 0.172739E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0661E+04 1.7185E+01 1.1498E+02 N 3554 BOND = 1411.9501 ANGLE = 3807.1759 DIHED = 5438.2459 VDWAALS = -3909.9583 EEL = -34861.7378 EGB = -7800.7888 1-4 VDW = 1818.3210 1-4 EEL = 23247.9151 RESTRAINT = 0.0000 ESURF = 187.8445 minimization completed, ENE= -.10661033E+05 RMS= 0.171847E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 679.05 ( 7.54% of Gen B) | Calc gb diag 5337.80 (59.29% of Gen B) | Calc gb off-diag 2985.42 (33.16% of Gen B) | Gen Born time 9002.28 (100.0% of Nonbo) | Nonbond force 9002.28 (100.0% of Force) | Bond/Angle/Dihedral 7.47 ( 0.08% of Force) | Force time 9009.76 (100.0% of Runmd) | Runmd Time 9009.76 (99.12% of Total) | Other 80.11 ( 0.88% of Total) | Total time 9089.89 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 00:30:16.472 on 10/20/2010 | Setup done at 00:30:18.594 on 10/20/2010 | Run done at 03:01:46.360 on 10/20/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/20/2010 at 00:30:17 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _lig.out.8 |INPCRD: 1XCK_chainA_MGATP_noWAT.inpcrd | PARM: 1XCK_chainA_MGATP_noWAT.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _lig.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 = 09/24/09 Time = 02:43:23 NATOM = 7879 NTYPES = 18 NBONH = 3991 MBONA = 3917 NTHETH = 9115 MTHETA = 5297 NPHIH = 17023 MPHIA = 12427 NHPARM = 0 NPARM = 0 NNB = 43422 NRES = 526 NBONA = 3917 NTHETA = 5297 NPHIA = 12427 NUMBND = 52 NUMANG = 108 NPTRA = 66 NATYP = 36 NPHB = 0 IFBOX = 0 NMXRS = 43 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 567848 | Hollerith 24165 | Integer 1061772 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 8678 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 -1.0832E+04 1.7282E+01 1.2391E+02 CZ 2872 BOND = 1426.0621 ANGLE = 3616.1763 DIHED = 5424.3095 VDWAALS = -3871.1603 EEL = -34975.7498 EGB = -7889.4465 1-4 VDW = 1822.6887 1-4 EEL = 23428.2235 RESTRAINT = 0.0000 ESURF = 186.4304 minimization completed, ENE= -.10832466E+05 RMS= 0.172822E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0776E+04 1.7335E+01 1.0448E+02 C 5664 BOND = 1452.9057 ANGLE = 3752.0461 DIHED = 5425.3090 VDWAALS = -3899.6622 EEL = -34903.7940 EGB = -7869.4304 1-4 VDW = 1763.7348 1-4 EEL = 23315.3121 RESTRAINT = 0.0000 ESURF = 187.2331 minimization completed, ENE= -.10776346E+05 RMS= 0.173354E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0650E+04 1.7526E+01 1.2045E+02 C 6878 BOND = 1490.7097 ANGLE = 3803.0970 DIHED = 5416.0015 VDWAALS = -3895.1098 EEL = -34968.5586 EGB = -7737.2866 1-4 VDW = 1759.1088 1-4 EEL = 23296.1066 RESTRAINT = 0.0000 ESURF = 186.1141 minimization completed, ENE= -.10649817E+05 RMS= 0.175255E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0748E+04 1.7226E+01 1.2749E+02 CD 6712 BOND = 1411.1537 ANGLE = 3664.2650 DIHED = 5429.2076 VDWAALS = -3912.7931 EEL = -34876.8573 EGB = -7849.0803 1-4 VDW = 1791.4615 1-4 EEL = 23408.7017 RESTRAINT = 0.0000 ESURF = 186.3922 minimization completed, ENE= -.10747549E+05 RMS= 0.172259E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0687E+04 1.7455E+01 1.2533E+02 CG 5392 BOND = 1442.6535 ANGLE = 3728.8865 DIHED = 5416.2995 VDWAALS = -3838.6141 EEL = -34931.7215 EGB = -7887.9936 1-4 VDW = 1807.3043 1-4 EEL = 23388.1297 RESTRAINT = 0.0000 ESURF = 187.6509 minimization completed, ENE= -.10687405E+05 RMS= 0.174554E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0766E+04 1.7382E+01 9.9444E+01 CD 3073 BOND = 1412.9121 ANGLE = 3727.3322 DIHED = 5395.3169 VDWAALS = -3895.1568 EEL = -34939.3877 EGB = -7822.6221 1-4 VDW = 1800.2183 1-4 EEL = 23369.6578 RESTRAINT = 0.0000 ESURF = 185.4689 minimization completed, ENE= -.10766260E+05 RMS= 0.173819E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0711E+04 1.7466E+01 1.0669E+02 C 1363 BOND = 1410.1533 ANGLE = 3711.5921 DIHED = 5386.9036 VDWAALS = -3906.4623 EEL = -34874.6225 EGB = -7884.0608 1-4 VDW = 1809.8460 1-4 EEL = 23449.1531 RESTRAINT = 0.0000 ESURF = 186.3617 minimization completed, ENE= -.10711136E+05 RMS= 0.174659E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0778E+04 1.7116E+01 1.0175E+02 C 278 BOND = 1411.0452 ANGLE = 3648.7392 DIHED = 5397.3633 VDWAALS = -3857.1912 EEL = -34960.6555 EGB = -7795.2425 1-4 VDW = 1808.7266 1-4 EEL = 23382.9376 RESTRAINT = 0.0000 ESURF = 185.8694 minimization completed, ENE= -.10778408E+05 RMS= 0.171163E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0669E+04 1.7192E+01 1.1668E+02 C 7374 BOND = 1397.0467 ANGLE = 3774.2169 DIHED = 5442.1495 VDWAALS = -3905.0620 EEL = -34880.5218 EGB = -7918.0012 1-4 VDW = 1829.3616 1-4 EEL = 23405.7546 RESTRAINT = 0.0000 ESURF = 185.6039 minimization completed, ENE= -.10669452E+05 RMS= 0.171920E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0777E+04 1.7367E+01 1.2018E+02 C 6853 BOND = 1433.2296 ANGLE = 3684.2109 DIHED = 5381.9382 VDWAALS = -3898.6699 EEL = -35017.9047 EGB = -7743.9755 1-4 VDW = 1806.1189 1-4 EEL = 23392.7046 RESTRAINT = 0.0000 ESURF = 185.7189 minimization completed, ENE= -.10776629E+05 RMS= 0.173672E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0820E+04 1.7264E+01 1.2401E+02 CZ 2965 BOND = 1389.8313 ANGLE = 3650.6367 DIHED = 5426.8918 VDWAALS = -3936.8909 EEL = -34998.0450 EGB = -7698.3164 1-4 VDW = 1814.1393 1-4 EEL = 23345.8551 RESTRAINT = 0.0000 ESURF = 185.6669 minimization completed, ENE= -.10820231E+05 RMS= 0.172644E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0826E+04 1.7229E+01 1.1584E+02 C 93 BOND = 1416.6610 ANGLE = 3692.0867 DIHED = 5400.5594 VDWAALS = -3904.6164 EEL = -35064.8574 EGB = -7683.1077 1-4 VDW = 1822.7030 1-4 EEL = 23309.4926 RESTRAINT = 0.0000 ESURF = 185.2684 minimization completed, ENE= -.10825810E+05 RMS= 0.172294E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0683E+04 1.7444E+01 1.0210E+02 C 196 BOND = 1423.7818 ANGLE = 3789.8379 DIHED = 5421.3395 VDWAALS = -3894.7122 EEL = -35100.2235 EGB = -7583.9979 1-4 VDW = 1799.5507 1-4 EEL = 23275.3660 RESTRAINT = 0.0000 ESURF = 186.4059 minimization completed, ENE= -.10682652E+05 RMS= 0.174438E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0660E+04 1.7635E+01 1.3635E+02 CD 4747 BOND = 1445.2123 ANGLE = 3826.5894 DIHED = 5417.0656 VDWAALS = -3916.4738 EEL = -35076.1058 EGB = -7722.3405 1-4 VDW = 1807.3054 1-4 EEL = 23372.1991 RESTRAINT = 0.0000 ESURF = 186.5393 minimization completed, ENE= -.10660009E+05 RMS= 0.176346E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0750E+04 1.7365E+01 1.3150E+02 N 3342 BOND = 1435.7319 ANGLE = 3681.5924 DIHED = 5415.1609 VDWAALS = -3920.9900 EEL = -35085.8899 EGB = -7644.6002 1-4 VDW = 1812.6776 1-4 EEL = 23372.3192 RESTRAINT = 0.0000 ESURF = 184.0963 minimization completed, ENE= -.10749902E+05 RMS= 0.173650E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0864E+04 1.7052E+01 1.1311E+02 C 7490 BOND = 1374.8541 ANGLE = 3650.1163 DIHED = 5385.2545 VDWAALS = -3921.7673 EEL = -35008.0722 EGB = -7746.2694 1-4 VDW = 1811.7939 1-4 EEL = 23403.9563 RESTRAINT = 0.0000 ESURF = 186.5273 minimization completed, ENE= -.10863606E+05 RMS= 0.170516E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0664E+04 1.7463E+01 1.2235E+02 C 5044 BOND = 1440.4452 ANGLE = 3776.8803 DIHED = 5442.2651 VDWAALS = -3933.2305 EEL = -35061.4241 EGB = -7648.5545 1-4 VDW = 1793.3917 1-4 EEL = 23341.7058 RESTRAINT = 0.0000 ESURF = 184.7040 minimization completed, ENE= -.10663817E+05 RMS= 0.174629E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0753E+04 1.7490E+01 1.1402E+02 C 5189 BOND = 1442.8661 ANGLE = 3652.8389 DIHED = 5467.1754 VDWAALS = -3842.4586 EEL = -35306.1278 EGB = -7483.8723 1-4 VDW = 1797.6160 1-4 EEL = 23334.1075 RESTRAINT = 0.0000 ESURF = 185.1795 minimization completed, ENE= -.10752675E+05 RMS= 0.174896E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0741E+04 1.7449E+01 1.3243E+02 CD 5774 BOND = 1444.7667 ANGLE = 3730.6511 DIHED = 5419.9125 VDWAALS = -3956.7243 EEL = -35046.0828 EGB = -7708.7397 1-4 VDW = 1800.1402 1-4 EEL = 23390.4478 RESTRAINT = 0.0000 ESURF = 184.7420 minimization completed, ENE= -.10740887E+05 RMS= 0.174491E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0859E+04 1.7108E+01 1.3175E+02 C 4617 BOND = 1402.5788 ANGLE = 3708.5053 DIHED = 5409.8267 VDWAALS = -3887.3920 EEL = -35179.6321 EGB = -7542.3274 1-4 VDW = 1777.3252 1-4 EEL = 23265.8102 RESTRAINT = 0.0000 ESURF = 186.7401 minimization completed, ENE= -.10858565E+05 RMS= 0.171078E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0825E+04 1.7543E+01 1.1469E+02 C 4859 BOND = 1426.8083 ANGLE = 3650.0850 DIHED = 5395.9674 VDWAALS = -3924.0715 EEL = -35238.1847 EGB = -7555.8554 1-4 VDW = 1797.2536 1-4 EEL = 23437.0812 RESTRAINT = 0.0000 ESURF = 186.1451 minimization completed, ENE= -.10824771E+05 RMS= 0.175426E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0723E+04 1.7270E+01 1.0713E+02 C 156 BOND = 1395.7870 ANGLE = 3715.6877 DIHED = 5470.7159 VDWAALS = -3902.2744 EEL = -35164.0180 EGB = -7646.4959 1-4 VDW = 1818.8463 1-4 EEL = 23401.8419 RESTRAINT = 0.0000 ESURF = 186.5760 minimization completed, ENE= -.10723334E+05 RMS= 0.172705E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0697E+04 1.7630E+01 1.1229E+02 CG 4342 BOND = 1451.2398 ANGLE = 3817.7149 DIHED = 5414.9796 VDWAALS = -3880.7147 EEL = -35278.9208 EGB = -7555.3814 1-4 VDW = 1783.3779 1-4 EEL = 23363.5088 RESTRAINT = 0.0000 ESURF = 187.2145 minimization completed, ENE= -.10696981E+05 RMS= 0.176299E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0672E+04 1.7468E+01 1.1574E+02 C 4270 BOND = 1426.5603 ANGLE = 3777.8855 DIHED = 5467.0331 VDWAALS = -3950.4745 EEL = -35126.7546 EGB = -7548.2448 1-4 VDW = 1787.1928 1-4 EEL = 23309.0758 RESTRAINT = 0.0000 ESURF = 186.0190 minimization completed, ENE= -.10671707E+05 RMS= 0.174681E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0839E+04 1.7121E+01 1.1176E+02 C 2142 BOND = 1371.0367 ANGLE = 3787.0438 DIHED = 5405.9460 VDWAALS = -3883.1495 EEL = -35358.3030 EGB = -7437.2199 1-4 VDW = 1769.8531 1-4 EEL = 23320.4693 RESTRAINT = 0.0000 ESURF = 185.5705 minimization completed, ENE= -.10838753E+05 RMS= 0.171212E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0676E+04 1.7451E+01 1.1812E+02 C 5315 BOND = 1424.0373 ANGLE = 3767.5813 DIHED = 5428.3822 VDWAALS = -3885.3560 EEL = -35255.7180 EGB = -7543.8635 1-4 VDW = 1794.2604 1-4 EEL = 23407.9028 RESTRAINT = 0.0000 ESURF = 186.3930 minimization completed, ENE= -.10676381E+05 RMS= 0.174514E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0717E+04 1.7248E+01 1.1105E+02 C 5122 BOND = 1419.2451 ANGLE = 3796.6625 DIHED = 5450.0684 VDWAALS = -3873.1923 EEL = -35147.7239 EGB = -7628.0470 1-4 VDW = 1768.3596 1-4 EEL = 23309.9493 RESTRAINT = 0.0000 ESURF = 187.8262 minimization completed, ENE= -.10716852E+05 RMS= 0.172477E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0829E+04 1.7225E+01 1.0833E+02 C 2301 BOND = 1423.4348 ANGLE = 3747.7286 DIHED = 5403.3669 VDWAALS = -3904.6419 EEL = -35146.6967 EGB = -7703.5957 1-4 VDW = 1770.0936 1-4 EEL = 23394.5779 RESTRAINT = 0.0000 ESURF = 187.2183 minimization completed, ENE= -.10828514E+05 RMS= 0.172253E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0775E+04 1.7224E+01 1.1441E+02 C 4034 BOND = 1434.2463 ANGLE = 3701.9191 DIHED = 5416.2629 VDWAALS = -3926.4273 EEL = -35049.9461 EGB = -7709.9793 1-4 VDW = 1800.2361 1-4 EEL = 23370.1523 RESTRAINT = 0.0000 ESURF = 188.1623 minimization completed, ENE= -.10775374E+05 RMS= 0.172237E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0796E+04 1.7191E+01 1.5797E+02 C 3568 BOND = 1420.3295 ANGLE = 3703.0480 DIHED = 5419.7247 VDWAALS = -3868.5478 EEL = -35133.4237 EGB = -7608.2041 1-4 VDW = 1778.1865 1-4 EEL = 23303.9377 RESTRAINT = 0.0000 ESURF = 188.7106 minimization completed, ENE= -.10796239E+05 RMS= 0.171911E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0707E+04 1.7458E+01 1.0261E+02 C 4551 BOND = 1417.2291 ANGLE = 3830.2230 DIHED = 5387.5647 VDWAALS = -3842.9058 EEL = -35137.4861 EGB = -7744.2037 1-4 VDW = 1804.4702 1-4 EEL = 23386.0616 RESTRAINT = 0.0000 ESURF = 191.5750 minimization completed, ENE= -.10707472E+05 RMS= 0.174580E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0834E+04 1.7305E+01 1.3661E+02 C 21 BOND = 1435.7396 ANGLE = 3684.2363 DIHED = 5433.3477 VDWAALS = -3869.9046 EEL = -35124.3152 EGB = -7713.2859 1-4 VDW = 1786.8132 1-4 EEL = 23342.9468 RESTRAINT = 0.0000 ESURF = 190.8491 minimization completed, ENE= -.10833573E+05 RMS= 0.173047E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0755E+04 1.7265E+01 1.1125E+02 CA 6933 BOND = 1425.7803 ANGLE = 3666.1774 DIHED = 5413.6553 VDWAALS = -3914.2829 EEL = -35107.1591 EGB = -7588.8897 1-4 VDW = 1801.0891 1-4 EEL = 23362.3861 RESTRAINT = 0.0000 ESURF = 186.6366 minimization completed, ENE= -.10754607E+05 RMS= 0.172649E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0830E+04 1.7084E+01 1.2949E+02 CG 3932 BOND = 1351.3574 ANGLE = 3780.3853 DIHED = 5417.0082 VDWAALS = -3879.2104 EEL = -35292.8742 EGB = -7533.4737 1-4 VDW = 1796.3870 1-4 EEL = 23345.1210 RESTRAINT = 0.0000 ESURF = 185.5678 minimization completed, ENE= -.10829732E+05 RMS= 0.170843E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0797E+04 1.7065E+01 1.0728E+02 C 5044 BOND = 1394.0870 ANGLE = 3758.2335 DIHED = 5413.5112 VDWAALS = -3895.1802 EEL = -35038.5641 EGB = -7714.4601 1-4 VDW = 1770.7175 1-4 EEL = 23326.8390 RESTRAINT = 0.0000 ESURF = 187.6261 minimization completed, ENE= -.10797190E+05 RMS= 0.170653E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0830E+04 1.7276E+01 1.3205E+02 C 2499 BOND = 1353.1898 ANGLE = 3680.4801 DIHED = 5363.0567 VDWAALS = -3882.0071 EEL = -35238.9139 EGB = -7530.9263 1-4 VDW = 1835.9105 1-4 EEL = 23403.3325 RESTRAINT = 0.0000 ESURF = 185.7425 minimization completed, ENE= -.10830135E+05 RMS= 0.172762E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0729E+04 1.7392E+01 1.0994E+02 CA 4076 BOND = 1402.6348 ANGLE = 3764.7499 DIHED = 5397.6775 VDWAALS = -3914.0795 EEL = -35178.4108 EGB = -7599.4217 1-4 VDW = 1833.8697 1-4 EEL = 23379.7529 RESTRAINT = 0.0000 ESURF = 184.5363 minimization completed, ENE= -.10728691E+05 RMS= 0.173917E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0719E+04 1.7217E+01 1.1791E+02 C 7511 BOND = 1373.5429 ANGLE = 3740.9947 DIHED = 5403.3550 VDWAALS = -3904.5594 EEL = -35114.2933 EGB = -7637.3993 1-4 VDW = 1836.9633 1-4 EEL = 23397.9852 RESTRAINT = 0.0000 ESURF = 184.8763 minimization completed, ENE= -.10718535E+05 RMS= 0.172175E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0822E+04 1.7250E+01 1.0628E+02 CD 2511 BOND = 1397.1630 ANGLE = 3634.9469 DIHED = 5438.9619 VDWAALS = -3874.8853 EEL = -35038.6322 EGB = -7753.3450 1-4 VDW = 1807.9963 1-4 EEL = 23379.8594 RESTRAINT = 0.0000 ESURF = 185.4353 minimization completed, ENE= -.10822500E+05 RMS= 0.172495E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0768E+04 1.7270E+01 1.0736E+02 C 5395 BOND = 1393.7861 ANGLE = 3796.6159 DIHED = 5384.8722 VDWAALS = -3903.8664 EEL = -35144.4545 EGB = -7666.1486 1-4 VDW = 1801.8812 1-4 EEL = 23383.6461 RESTRAINT = 0.0000 ESURF = 185.2827 minimization completed, ENE= -.10768385E+05 RMS= 0.172699E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0813E+04 1.7307E+01 1.0798E+02 N 2258 BOND = 1411.3417 ANGLE = 3731.1941 DIHED = 5372.8046 VDWAALS = -3892.4431 EEL = -34972.6393 EGB = -7799.2633 1-4 VDW = 1787.2321 1-4 EEL = 23364.1797 RESTRAINT = 0.0000 ESURF = 184.6469 minimization completed, ENE= -.10812947E+05 RMS= 0.173074E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0838E+04 1.7071E+01 1.1865E+02 C 620 BOND = 1376.3616 ANGLE = 3698.6495 DIHED = 5426.4419 VDWAALS = -3896.9546 EEL = -35005.3978 EGB = -7818.9813 1-4 VDW = 1797.5252 1-4 EEL = 23397.0045 RESTRAINT = 0.0000 ESURF = 187.2861 minimization completed, ENE= -.10838065E+05 RMS= 0.170714E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0732E+04 1.7603E+01 1.1255E+02 CD1 103 BOND = 1419.8317 ANGLE = 3707.7534 DIHED = 5422.0671 VDWAALS = -3900.6418 EEL = -34977.2892 EGB = -7784.0151 1-4 VDW = 1791.2181 1-4 EEL = 23400.5492 RESTRAINT = 0.0000 ESURF = 188.6511 minimization completed, ENE= -.10731875E+05 RMS= 0.176033E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0771E+04 1.7327E+01 1.1392E+02 N 374 BOND = 1440.2187 ANGLE = 3725.4773 DIHED = 5390.0583 VDWAALS = -3779.0068 EEL = -35212.8066 EGB = -7661.8105 1-4 VDW = 1785.6170 1-4 EEL = 23351.9325 RESTRAINT = 0.0000 ESURF = 189.2741 minimization completed, ENE= -.10771046E+05 RMS= 0.173267E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0698E+04 1.7233E+01 1.1178E+02 C 6540 BOND = 1412.3067 ANGLE = 3714.3550 DIHED = 5440.3802 VDWAALS = -3912.6492 EEL = -34913.4836 EGB = -7822.2111 1-4 VDW = 1821.1952 1-4 EEL = 23374.3425 RESTRAINT = 0.0000 ESURF = 187.3992 minimization completed, ENE= -.10698365E+05 RMS= 0.172329E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0901E+04 1.7336E+01 1.0255E+02 CD 3539 BOND = 1406.0667 ANGLE = 3644.1567 DIHED = 5380.8741 VDWAALS = -3886.7569 EEL = -34983.5899 EGB = -7811.6521 1-4 VDW = 1806.8004 1-4 EEL = 23354.6641 RESTRAINT = 0.0000 ESURF = 188.4232 minimization completed, ENE= -.10901014E+05 RMS= 0.173358E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0759E+04 1.7541E+01 1.0630E+02 CD 1499 BOND = 1451.4564 ANGLE = 3718.0695 DIHED = 5383.8357 VDWAALS = -3876.9742 EEL = -34935.0122 EGB = -7794.6625 1-4 VDW = 1800.1979 1-4 EEL = 23305.9385 RESTRAINT = 0.0000 ESURF = 187.8126 minimization completed, ENE= -.10759338E+05 RMS= 0.175408E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0776E+04 1.7463E+01 1.2480E+02 C 4551 BOND = 1461.0389 ANGLE = 3693.3364 DIHED = 5400.8980 VDWAALS = -3906.7063 EEL = -34899.3772 EGB = -7829.3113 1-4 VDW = 1812.0068 1-4 EEL = 23304.6598 RESTRAINT = 0.0000 ESURF = 187.3379 minimization completed, ENE= -.10776117E+05 RMS= 0.174625E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0675E+04 1.7186E+01 1.2408E+02 C 620 BOND = 1398.1615 ANGLE = 3799.4474 DIHED = 5413.9608 VDWAALS = -3858.2810 EEL = -35018.8708 EGB = -7686.9056 1-4 VDW = 1807.9422 1-4 EEL = 23282.3060 RESTRAINT = 0.0000 ESURF = 186.9565 minimization completed, ENE= -.10675283E+05 RMS= 0.171864E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0728E+04 1.7262E+01 1.5131E+02 CZ 7561 BOND = 1434.5176 ANGLE = 3760.0212 DIHED = 5444.6256 VDWAALS = -3830.7832 EEL = -35087.2043 EGB = -7650.5327 1-4 VDW = 1805.6990 1-4 EEL = 23206.9497 RESTRAINT = 0.0000 ESURF = 188.8527 minimization completed, ENE= -.10727854E+05 RMS= 0.172617E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 689.41 ( 7.66% of Gen B) | Calc gb diag 5326.27 (59.19% of Gen B) | Calc gb off-diag 2983.34 (33.15% of Gen B) | Gen Born time 8999.03 (100.0% of Nonbo) | Nonbond force 8999.03 (100.0% of Force) | Bond/Angle/Dihedral 8.17 ( 0.09% of Force) | Force time 9007.20 (100.0% of Runmd) | Runmd Time 9007.20 (99.10% of Total) | Other 82.10 ( 0.90% of Total) | Total time 9089.33 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 00:30:16.470 on 10/20/2010 | Setup done at 00:30:18.894 on 10/20/2010 | Run done at 03:01:45.797 on 10/20/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/20/2010 at 00:30:16 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _lig.out.7 |INPCRD: 1XCK_chainA_MGATP_noWAT.inpcrd | PARM: 1XCK_chainA_MGATP_noWAT.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _lig.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 = 09/24/09 Time = 02:43:23 NATOM = 7879 NTYPES = 18 NBONH = 3991 MBONA = 3917 NTHETH = 9115 MTHETA = 5297 NPHIH = 17023 MPHIA = 12427 NHPARM = 0 NPARM = 0 NNB = 43422 NRES = 526 NBONA = 3917 NTHETA = 5297 NPHIA = 12427 NUMBND = 52 NUMANG = 108 NPTRA = 66 NATYP = 36 NPHB = 0 IFBOX = 0 NMXRS = 43 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 567848 | Hollerith 24165 | Integer 1061772 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 8678 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 -1.0717E+04 1.7550E+01 1.1108E+02 C 792 BOND = 1452.6286 ANGLE = 3742.4560 DIHED = 5451.7656 VDWAALS = -3870.4062 EEL = -35030.1113 EGB = -7680.8305 1-4 VDW = 1783.8472 1-4 EEL = 23249.8158 RESTRAINT = 0.0000 ESURF = 183.6232 minimization completed, ENE= -.10717212E+05 RMS= 0.175497E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0611E+04 1.7442E+01 1.1167E+02 C 2641 BOND = 1426.1933 ANGLE = 3794.2924 DIHED = 5466.9287 VDWAALS = -3901.1419 EEL = -34997.3773 EGB = -7734.2380 1-4 VDW = 1808.8381 1-4 EEL = 23340.6268 RESTRAINT = 0.0000 ESURF = 185.0982 minimization completed, ENE= -.10610780E+05 RMS= 0.174416E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0712E+04 1.7616E+01 1.2236E+02 N 2144 BOND = 1434.9392 ANGLE = 3791.7725 DIHED = 5423.5941 VDWAALS = -3932.9325 EEL = -34961.4457 EGB = -7720.9726 1-4 VDW = 1800.5311 1-4 EEL = 23269.9012 RESTRAINT = 0.0000 ESURF = 182.5543 minimization completed, ENE= -.10712058E+05 RMS= 0.176161E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0776E+04 1.7525E+01 1.5273E+02 C 2634 BOND = 1460.3579 ANGLE = 3732.6303 DIHED = 5421.2511 VDWAALS = -3923.2586 EEL = -35089.8053 EGB = -7636.2672 1-4 VDW = 1770.2450 1-4 EEL = 23305.0933 RESTRAINT = 0.0000 ESURF = 183.7980 minimization completed, ENE= -.10775956E+05 RMS= 0.175254E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0808E+04 1.7213E+01 1.3819E+02 C 5615 BOND = 1354.0126 ANGLE = 3759.9099 DIHED = 5434.6921 VDWAALS = -3927.3875 EEL = -35147.5941 EGB = -7622.5381 1-4 VDW = 1807.0741 1-4 EEL = 23351.5113 RESTRAINT = 0.0000 ESURF = 182.0383 minimization completed, ENE= -.10808281E+05 RMS= 0.172127E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0873E+04 1.7340E+01 1.0770E+02 C 3172 BOND = 1427.4894 ANGLE = 3642.1255 DIHED = 5400.7452 VDWAALS = -3939.4624 EEL = -35220.7298 EGB = -7551.0119 1-4 VDW = 1798.7055 1-4 EEL = 23385.6735 RESTRAINT = 0.0000 ESURF = 183.2272 minimization completed, ENE= -.10873238E+05 RMS= 0.173396E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0677E+04 1.7300E+01 1.0218E+02 N 5164 BOND = 1412.7955 ANGLE = 3739.9216 DIHED = 5491.5190 VDWAALS = -3937.9613 EEL = -35114.7615 EGB = -7643.4555 1-4 VDW = 1804.2953 1-4 EEL = 23387.6688 RESTRAINT = 0.0000 ESURF = 183.4363 minimization completed, ENE= -.10676542E+05 RMS= 0.172997E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0664E+04 1.7419E+01 1.1355E+02 CA 2202 BOND = 1418.7207 ANGLE = 3808.3253 DIHED = 5443.0510 VDWAALS = -3873.1166 EEL = -35073.5596 EGB = -7748.3320 1-4 VDW = 1788.7987 1-4 EEL = 23386.9295 RESTRAINT = 0.0000 ESURF = 184.9914 minimization completed, ENE= -.10664192E+05 RMS= 0.174191E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0723E+04 1.7260E+01 1.1659E+02 CG 369 BOND = 1415.1729 ANGLE = 3716.8750 DIHED = 5462.3282 VDWAALS = -3924.0056 EEL = -35061.3789 EGB = -7707.9732 1-4 VDW = 1799.5046 1-4 EEL = 23390.3700 RESTRAINT = 0.0000 ESURF = 185.6769 minimization completed, ENE= -.10723430E+05 RMS= 0.172596E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0698E+04 1.7262E+01 1.0048E+02 N 6651 BOND = 1361.6537 ANGLE = 3750.5459 DIHED = 5410.6495 VDWAALS = -3829.1810 EEL = -35181.0013 EGB = -7677.7827 1-4 VDW = 1826.3140 1-4 EEL = 23454.9447 RESTRAINT = 0.0000 ESURF = 185.6676 minimization completed, ENE= -.10698190E+05 RMS= 0.172620E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0763E+04 1.7102E+01 1.0828E+02 C 1261 BOND = 1396.0904 ANGLE = 3754.3256 DIHED = 5450.5653 VDWAALS = -3920.1393 EEL = -34991.7435 EGB = -7752.0674 1-4 VDW = 1794.6424 1-4 EEL = 23320.1655 RESTRAINT = 0.0000 ESURF = 185.1145 minimization completed, ENE= -.10763047E+05 RMS= 0.171021E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0744E+04 1.7241E+01 1.2898E+02 C 1560 BOND = 1430.1479 ANGLE = 3699.9018 DIHED = 5455.4923 VDWAALS = -3895.6059 EEL = -34917.2454 EGB = -7752.8705 1-4 VDW = 1785.6811 1-4 EEL = 23265.2140 RESTRAINT = 0.0000 ESURF = 185.6516 minimization completed, ENE= -.10743633E+05 RMS= 0.172414E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0712E+04 1.7599E+01 1.2026E+02 CD 3439 BOND = 1426.8364 ANGLE = 3701.2056 DIHED = 5416.7208 VDWAALS = -3880.8298 EEL = -35255.6001 EGB = -7472.5332 1-4 VDW = 1823.2197 1-4 EEL = 23347.0382 RESTRAINT = 0.0000 ESURF = 182.0970 minimization completed, ENE= -.10711845E+05 RMS= 0.175990E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0866E+04 1.7187E+01 1.1170E+02 C 642 BOND = 1386.6873 ANGLE = 3656.2312 DIHED = 5429.1527 VDWAALS = -3913.7627 EEL = -35266.1392 EGB = -7499.7323 1-4 VDW = 1777.6191 1-4 EEL = 23381.1052 RESTRAINT = 0.0000 ESURF = 182.8357 minimization completed, ENE= -.10866003E+05 RMS= 0.171873E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0696E+04 1.7460E+01 1.2626E+02 C 6526 BOND = 1457.9791 ANGLE = 3716.1982 DIHED = 5443.0881 VDWAALS = -3881.2606 EEL = -35031.1811 EGB = -7655.7703 1-4 VDW = 1790.1939 1-4 EEL = 23280.3067 RESTRAINT = 0.0000 ESURF = 184.3171 minimization completed, ENE= -.10696129E+05 RMS= 0.174596E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0660E+04 1.7400E+01 1.1973E+02 CD 5056 BOND = 1460.6626 ANGLE = 3749.9264 DIHED = 5419.2270 VDWAALS = -3880.9883 EEL = -35171.1866 EGB = -7628.9374 1-4 VDW = 1823.6781 1-4 EEL = 23384.3045 RESTRAINT = 0.0000 ESURF = 183.6587 minimization completed, ENE= -.10659655E+05 RMS= 0.174001E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0736E+04 1.7307E+01 1.1692E+02 CA 6331 BOND = 1408.7290 ANGLE = 3730.9464 DIHED = 5460.2756 VDWAALS = -3908.3479 EEL = -35015.4694 EGB = -7730.6342 1-4 VDW = 1786.2665 1-4 EEL = 23347.8971 RESTRAINT = 0.0000 ESURF = 184.7348 minimization completed, ENE= -.10735602E+05 RMS= 0.173071E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0707E+04 1.7449E+01 1.1129E+02 C 5993 BOND = 1434.1467 ANGLE = 3796.7992 DIHED = 5436.9004 VDWAALS = -3928.7367 EEL = -34864.3584 EGB = -7880.3956 1-4 VDW = 1793.1436 1-4 EEL = 23320.0840 RESTRAINT = 0.0000 ESURF = 185.1152 minimization completed, ENE= -.10707302E+05 RMS= 0.174492E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0818E+04 1.6976E+01 1.0724E+02 N 3174 BOND = 1398.1901 ANGLE = 3733.8131 DIHED = 5439.1993 VDWAALS = -3935.2533 EEL = -34842.3386 EGB = -7852.6910 1-4 VDW = 1771.3041 1-4 EEL = 23284.8691 RESTRAINT = 0.0000 ESURF = 185.1255 minimization completed, ENE= -.10817782E+05 RMS= 0.169765E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0736E+04 1.7423E+01 1.2345E+02 CG 7309 BOND = 1448.3573 ANGLE = 3727.2702 DIHED = 5425.6057 VDWAALS = -3922.7233 EEL = -35086.6295 EGB = -7701.7562 1-4 VDW = 1813.6558 1-4 EEL = 23376.9296 RESTRAINT = 0.0000 ESURF = 183.5372 minimization completed, ENE= -.10735753E+05 RMS= 0.174235E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0723E+04 1.7369E+01 1.1781E+02 N 374 BOND = 1443.5127 ANGLE = 3766.6110 DIHED = 5413.1347 VDWAALS = -3878.3813 EEL = -34946.4275 EGB = -7791.0217 1-4 VDW = 1787.3999 1-4 EEL = 23295.9202 RESTRAINT = 0.0000 ESURF = 186.2799 minimization completed, ENE= -.10722972E+05 RMS= 0.173695E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0764E+04 1.7397E+01 1.0448E+02 N 452 BOND = 1420.9173 ANGLE = 3662.8222 DIHED = 5385.2964 VDWAALS = -3871.7942 EEL = -35035.1923 EGB = -7733.5249 1-4 VDW = 1838.8789 1-4 EEL = 23385.6160 RESTRAINT = 0.0000 ESURF = 183.3773 minimization completed, ENE= -.10763603E+05 RMS= 0.173968E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0690E+04 1.7461E+01 1.1577E+02 C 5557 BOND = 1413.9328 ANGLE = 3774.3269 DIHED = 5439.9104 VDWAALS = -3911.6362 EEL = -34839.9447 EGB = -7802.4275 1-4 VDW = 1805.3225 1-4 EEL = 23246.7358 RESTRAINT = 0.0000 ESURF = 183.7407 minimization completed, ENE= -.10690039E+05 RMS= 0.174609E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0773E+04 1.7300E+01 1.2839E+02 CG 7090 BOND = 1415.2636 ANGLE = 3718.3879 DIHED = 5438.4379 VDWAALS = -3897.3355 EEL = -34902.9064 EGB = -7825.5405 1-4 VDW = 1808.6369 1-4 EEL = 23288.2652 RESTRAINT = 0.0000 ESURF = 183.3405 minimization completed, ENE= -.10773450E+05 RMS= 0.172995E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0865E+04 1.7063E+01 1.2117E+02 C 6540 BOND = 1378.3004 ANGLE = 3708.0817 DIHED = 5426.9002 VDWAALS = -3896.5131 EEL = -34805.0872 EGB = -7882.8955 1-4 VDW = 1773.9567 1-4 EEL = 23248.1755 RESTRAINT = 0.0000 ESURF = 183.8940 minimization completed, ENE= -.10865187E+05 RMS= 0.170633E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0773E+04 1.7302E+01 1.0471E+02 C 3157 BOND = 1389.4325 ANGLE = 3730.1777 DIHED = 5420.1198 VDWAALS = -3889.9748 EEL = -35021.3803 EGB = -7784.4956 1-4 VDW = 1814.8515 1-4 EEL = 23383.5030 RESTRAINT = 0.0000 ESURF = 184.3585 minimization completed, ENE= -.10773408E+05 RMS= 0.173016E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0719E+04 1.7603E+01 1.3135E+02 C 3138 BOND = 1418.8335 ANGLE = 3804.6197 DIHED = 5436.7775 VDWAALS = -3904.0575 EEL = -34847.0469 EGB = -7889.3184 1-4 VDW = 1778.3966 1-4 EEL = 23298.1631 RESTRAINT = 0.0000 ESURF = 184.3021 minimization completed, ENE= -.10719330E+05 RMS= 0.176035E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0758E+04 1.7218E+01 1.2024E+02 CD 5297 BOND = 1382.3979 ANGLE = 3758.2913 DIHED = 5420.6702 VDWAALS = -3966.7052 EEL = -34809.3553 EGB = -7828.2849 1-4 VDW = 1795.2177 1-4 EEL = 23306.0997 RESTRAINT = 0.0000 ESURF = 183.6097 minimization completed, ENE= -.10758059E+05 RMS= 0.172177E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0847E+04 1.6984E+01 1.0440E+02 N 1061 BOND = 1386.4386 ANGLE = 3687.1446 DIHED = 5406.1928 VDWAALS = -3892.7926 EEL = -34853.2198 EGB = -7759.1611 1-4 VDW = 1795.3158 1-4 EEL = 23200.5568 RESTRAINT = 0.0000 ESURF = 182.4757 minimization completed, ENE= -.10847049E+05 RMS= 0.169841E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0765E+04 1.7344E+01 1.0829E+02 C 5557 BOND = 1396.3377 ANGLE = 3759.9555 DIHED = 5449.6540 VDWAALS = -3951.4900 EEL = -34944.2460 EGB = -7764.5469 1-4 VDW = 1801.1087 1-4 EEL = 23305.1244 RESTRAINT = 0.0000 ESURF = 183.1462 minimization completed, ENE= -.10764956E+05 RMS= 0.173437E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0821E+04 1.7174E+01 1.0503E+02 C 1398 BOND = 1404.5919 ANGLE = 3767.5808 DIHED = 5399.8011 VDWAALS = -3922.3693 EEL = -34979.9705 EGB = -7740.0763 1-4 VDW = 1787.6454 1-4 EEL = 23276.8206 RESTRAINT = 0.0000 ESURF = 184.9200 minimization completed, ENE= -.10821056E+05 RMS= 0.171735E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0769E+04 1.7294E+01 1.2383E+02 CA 5166 BOND = 1416.9550 ANGLE = 3753.2725 DIHED = 5418.0088 VDWAALS = -3874.2496 EEL = -35145.0122 EGB = -7644.7911 1-4 VDW = 1801.0893 1-4 EEL = 23321.0382 RESTRAINT = 0.0000 ESURF = 184.8036 minimization completed, ENE= -.10768885E+05 RMS= 0.172936E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0701E+04 1.7348E+01 1.4574E+02 C 3872 BOND = 1387.1919 ANGLE = 3811.4248 DIHED = 5416.7514 VDWAALS = -3879.8486 EEL = -35066.6092 EGB = -7633.8689 1-4 VDW = 1778.7778 1-4 EEL = 23301.3539 RESTRAINT = 0.0000 ESURF = 183.8714 minimization completed, ENE= -.10700956E+05 RMS= 0.173483E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0786E+04 1.7268E+01 1.1296E+02 C 2499 BOND = 1412.1197 ANGLE = 3673.9840 DIHED = 5428.1738 VDWAALS = -3917.7660 EEL = -34964.1888 EGB = -7680.4655 1-4 VDW = 1800.7557 1-4 EEL = 23277.3060 RESTRAINT = 0.0000 ESURF = 184.5200 minimization completed, ENE= -.10785561E+05 RMS= 0.172680E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0759E+04 1.7327E+01 1.1619E+02 C 5162 BOND = 1417.1439 ANGLE = 3691.1159 DIHED = 5428.0116 VDWAALS = -3865.5327 EEL = -34983.3936 EGB = -7751.2077 1-4 VDW = 1800.3238 1-4 EEL = 23317.9960 RESTRAINT = 0.0000 ESURF = 186.7565 minimization completed, ENE= -.10758786E+05 RMS= 0.173268E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0733E+04 1.7352E+01 1.1016E+02 CA 6243 BOND = 1432.4589 ANGLE = 3666.9477 DIHED = 5413.5672 VDWAALS = -3881.0223 EEL = -34931.0616 EGB = -7725.3153 1-4 VDW = 1813.2952 1-4 EEL = 23291.3707 RESTRAINT = 0.0000 ESURF = 186.4687 minimization completed, ENE= -.10733291E+05 RMS= 0.173520E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0747E+04 1.7375E+01 1.2502E+02 C 3061 BOND = 1363.7065 ANGLE = 3778.1854 DIHED = 5418.8572 VDWAALS = -3858.5502 EEL = -35096.1868 EGB = -7684.8197 1-4 VDW = 1807.3668 1-4 EEL = 23337.3194 RESTRAINT = 0.0000 ESURF = 186.8133 minimization completed, ENE= -.10747308E+05 RMS= 0.173749E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0804E+04 1.7401E+01 1.2615E+02 NE 3983 BOND = 1431.8217 ANGLE = 3631.4549 DIHED = 5415.8550 VDWAALS = -3861.1422 EEL = -35014.1188 EGB = -7689.0072 1-4 VDW = 1811.9411 1-4 EEL = 23282.9028 RESTRAINT = 0.0000 ESURF = 185.9596 minimization completed, ENE= -.10804333E+05 RMS= 0.174014E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0662E+04 1.7215E+01 1.1634E+02 CA 7619 BOND = 1369.7834 ANGLE = 3815.4913 DIHED = 5461.7037 VDWAALS = -3909.3804 EEL = -34766.4523 EGB = -7910.7424 1-4 VDW = 1792.1066 1-4 EEL = 23299.4920 RESTRAINT = 0.0000 ESURF = 186.0202 minimization completed, ENE= -.10661978E+05 RMS= 0.172155E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0722E+04 1.7559E+01 1.3578E+02 C 1278 BOND = 1466.9004 ANGLE = 3678.8852 DIHED = 5439.2673 VDWAALS = -3947.0430 EEL = -34854.2547 EGB = -7867.5455 1-4 VDW = 1804.4328 1-4 EEL = 23372.0328 RESTRAINT = 0.0000 ESURF = 185.0885 minimization completed, ENE= -.10722236E+05 RMS= 0.175588E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0744E+04 1.7333E+01 1.1721E+02 C2 7868 BOND = 1402.3210 ANGLE = 3717.0886 DIHED = 5423.0975 VDWAALS = -3870.9541 EEL = -35017.0715 EGB = -7782.6120 1-4 VDW = 1802.8766 1-4 EEL = 23394.5151 RESTRAINT = 0.0000 ESURF = 186.8205 minimization completed, ENE= -.10743918E+05 RMS= 0.173329E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0713E+04 1.7349E+01 1.1230E+02 C 1278 BOND = 1429.7661 ANGLE = 3693.2118 DIHED = 5445.0215 VDWAALS = -3913.8210 EEL = -35017.8705 EGB = -7733.4601 1-4 VDW = 1816.6316 1-4 EEL = 23379.7882 RESTRAINT = 0.0000 ESURF = 187.2972 minimization completed, ENE= -.10713435E+05 RMS= 0.173493E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0737E+04 1.7318E+01 1.1633E+02 C 1069 BOND = 1417.2030 ANGLE = 3731.0168 DIHED = 5436.4064 VDWAALS = -3873.4342 EEL = -35029.3028 EGB = -7743.9088 1-4 VDW = 1821.2404 1-4 EEL = 23317.5490 RESTRAINT = 0.0000 ESURF = 186.4879 minimization completed, ENE= -.10736742E+05 RMS= 0.173175E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0648E+04 1.7547E+01 1.2283E+02 CD 1153 BOND = 1467.2346 ANGLE = 3714.2511 DIHED = 5427.0012 VDWAALS = -3898.7989 EEL = -34957.3619 EGB = -7743.8779 1-4 VDW = 1820.5846 1-4 EEL = 23337.0059 RESTRAINT = 0.0000 ESURF = 185.7937 minimization completed, ENE= -.10648168E+05 RMS= 0.175475E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0761E+04 1.7230E+01 1.3298E+02 N 6041 BOND = 1395.5577 ANGLE = 3761.5853 DIHED = 5409.3154 VDWAALS = -3927.5830 EEL = -34883.2437 EGB = -7848.2523 1-4 VDW = 1810.6426 1-4 EEL = 23335.3826 RESTRAINT = 0.0000 ESURF = 185.6894 minimization completed, ENE= -.10760906E+05 RMS= 0.172304E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0708E+04 1.7468E+01 1.2231E+02 N 4553 BOND = 1427.6594 ANGLE = 3786.8430 DIHED = 5436.2890 VDWAALS = -3928.5562 EEL = -34826.7315 EGB = -7921.7042 1-4 VDW = 1784.3424 1-4 EEL = 23347.8278 RESTRAINT = 0.0000 ESURF = 186.1509 minimization completed, ENE= -.10707879E+05 RMS= 0.174676E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0668E+04 1.7323E+01 9.8792E+01 C 3819 BOND = 1412.9752 ANGLE = 3760.5028 DIHED = 5428.8733 VDWAALS = -3906.8467 EEL = -34984.4328 EGB = -7758.8717 1-4 VDW = 1820.0958 1-4 EEL = 23373.0051 RESTRAINT = 0.0000 ESURF = 186.7283 minimization completed, ENE= -.10667971E+05 RMS= 0.173227E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0735E+04 1.7541E+01 1.1347E+02 C 7632 BOND = 1442.7427 ANGLE = 3746.4679 DIHED = 5438.3969 VDWAALS = -3940.2742 EEL = -34953.2758 EGB = -7793.1787 1-4 VDW = 1809.4083 1-4 EEL = 23328.7840 RESTRAINT = 0.0000 ESURF = 186.2314 minimization completed, ENE= -.10734698E+05 RMS= 0.175413E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0798E+04 1.7208E+01 1.2230E+02 CG 7383 BOND = 1442.4863 ANGLE = 3748.5595 DIHED = 5431.5077 VDWAALS = -3930.6924 EEL = -35023.4395 EGB = -7696.1662 1-4 VDW = 1763.3713 1-4 EEL = 23280.5816 RESTRAINT = 0.0000 ESURF = 186.0306 minimization completed, ENE= -.10797761E+05 RMS= 0.172084E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0804E+04 1.7254E+01 1.2891E+02 C 372 BOND = 1410.1147 ANGLE = 3717.6957 DIHED = 5405.1363 VDWAALS = -3888.0746 EEL = -35057.8155 EGB = -7764.1101 1-4 VDW = 1799.2245 1-4 EEL = 23387.1572 RESTRAINT = 0.0000 ESURF = 186.8162 minimization completed, ENE= -.10803856E+05 RMS= 0.172539E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 690.84 ( 7.67% of Gen B) | Calc gb diag 5345.84 (59.39% of Gen B) | Calc gb off-diag 2964.62 (32.94% of Gen B) | Gen Born time 9001.31 (100.0% of Nonbo) | Nonbond force 9001.31 (100.0% of Force) | Bond/Angle/Dihedral 6.36 ( 0.07% of Force) | Force time 9007.67 (100.0% of Runmd) | Runmd Time 9007.67 (98.99% of Total) | Other 91.60 ( 1.01% of Total) | Total time 9099.32 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 00:30:16.470 on 10/20/2010 | Setup done at 00:30:17.280 on 10/20/2010 | Run done at 03:01:55.786 on 10/20/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/20/2010 at 00:30:16 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _lig.out.6 |INPCRD: 1XCK_chainA_MGATP_noWAT.inpcrd | PARM: 1XCK_chainA_MGATP_noWAT.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _lig.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 = 09/24/09 Time = 02:43:23 NATOM = 7879 NTYPES = 18 NBONH = 3991 MBONA = 3917 NTHETH = 9115 MTHETA = 5297 NPHIH = 17023 MPHIA = 12427 NHPARM = 0 NPARM = 0 NNB = 43422 NRES = 526 NBONA = 3917 NTHETA = 5297 NPHIA = 12427 NUMBND = 52 NUMANG = 108 NPTRA = 66 NATYP = 36 NPHB = 0 IFBOX = 0 NMXRS = 43 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 567848 | Hollerith 24165 | Integer 1061772 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 8678 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 -1.0723E+04 1.7509E+01 1.2842E+02 C 6029 BOND = 1407.9355 ANGLE = 3665.9601 DIHED = 5444.1926 VDWAALS = -3874.2765 EEL = -35307.6811 EGB = -7501.3893 1-4 VDW = 1844.7179 1-4 EEL = 23413.0335 RESTRAINT = 0.0000 ESURF = 184.9436 minimization completed, ENE= -.10722564E+05 RMS= 0.175089E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0729E+04 1.7415E+01 1.2252E+02 C 6128 BOND = 1427.5598 ANGLE = 3741.2078 DIHED = 5473.2692 VDWAALS = -3914.1325 EEL = -35145.5740 EGB = -7633.3135 1-4 VDW = 1796.2913 1-4 EEL = 23341.5493 RESTRAINT = 0.0000 ESURF = 184.3313 minimization completed, ENE= -.10728811E+05 RMS= 0.174152E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0805E+04 1.7122E+01 1.0361E+02 C 2723 BOND = 1410.7734 ANGLE = 3723.9186 DIHED = 5411.7563 VDWAALS = -3881.7026 EEL = -35138.8049 EGB = -7645.3886 1-4 VDW = 1802.1510 1-4 EEL = 23328.1935 RESTRAINT = 0.0000 ESURF = 183.8167 minimization completed, ENE= -.10805287E+05 RMS= 0.171220E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0838E+04 1.7212E+01 1.5602E+02 C 7632 BOND = 1357.5187 ANGLE = 3776.4947 DIHED = 5431.9047 VDWAALS = -3940.1212 EEL = -35203.7217 EGB = -7561.9020 1-4 VDW = 1763.9048 1-4 EEL = 23352.9323 RESTRAINT = 0.0000 ESURF = 184.6003 minimization completed, ENE= -.10838389E+05 RMS= 0.172119E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0677E+04 1.7436E+01 1.1113E+02 CD 6897 BOND = 1422.2639 ANGLE = 3743.0872 DIHED = 5430.3976 VDWAALS = -3892.2288 EEL = -34987.2787 EGB = -7750.2067 1-4 VDW = 1806.2416 1-4 EEL = 23366.4590 RESTRAINT = 0.0000 ESURF = 184.2133 minimization completed, ENE= -.10677052E+05 RMS= 0.174358E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0687E+04 1.7353E+01 1.0799E+02 CA 2911 BOND = 1452.0530 ANGLE = 3737.5680 DIHED = 5460.1090 VDWAALS = -3942.4157 EEL = -34937.6691 EGB = -7753.8282 1-4 VDW = 1772.1891 1-4 EEL = 23342.2716 RESTRAINT = 0.0000 ESURF = 182.9714 minimization completed, ENE= -.10686751E+05 RMS= 0.173526E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0690E+04 1.7384E+01 1.2105E+02 C 3508 BOND = 1430.0859 ANGLE = 3739.0255 DIHED = 5437.2614 VDWAALS = -3893.2816 EEL = -35036.0496 EGB = -7765.0770 1-4 VDW = 1808.1270 1-4 EEL = 23404.5648 RESTRAINT = 0.0000 ESURF = 185.0484 minimization completed, ENE= -.10690295E+05 RMS= 0.173842E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0827E+04 1.7105E+01 1.0198E+02 CA 6822 BOND = 1378.5647 ANGLE = 3680.3449 DIHED = 5430.9953 VDWAALS = -3885.8420 EEL = -35109.5676 EGB = -7730.7637 1-4 VDW = 1822.7459 1-4 EEL = 23402.2912 RESTRAINT = 0.0000 ESURF = 184.2680 minimization completed, ENE= -.10826963E+05 RMS= 0.171052E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0664E+04 1.7609E+01 1.0155E+02 C 4082 BOND = 1488.5035 ANGLE = 3701.6025 DIHED = 5447.9161 VDWAALS = -3884.6317 EEL = -35192.8628 EGB = -7497.4181 1-4 VDW = 1780.0037 1-4 EEL = 23309.5998 RESTRAINT = 0.0000 ESURF = 183.3623 minimization completed, ENE= -.10663925E+05 RMS= 0.176087E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0726E+04 1.7186E+01 1.0154E+02 C 6700 BOND = 1390.5547 ANGLE = 3667.7579 DIHED = 5466.3979 VDWAALS = -3856.4173 EEL = -35174.9179 EGB = -7596.1989 1-4 VDW = 1834.8001 1-4 EEL = 23357.5208 RESTRAINT = 0.0000 ESURF = 184.2613 minimization completed, ENE= -.10726241E+05 RMS= 0.171858E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0619E+04 1.7259E+01 1.0107E+02 C 1634 BOND = 1382.8571 ANGLE = 3822.0086 DIHED = 5445.1272 VDWAALS = -3893.3304 EEL = -35104.1676 EGB = -7585.7998 1-4 VDW = 1810.1108 1-4 EEL = 23320.1056 RESTRAINT = 0.0000 ESURF = 184.1807 minimization completed, ENE= -.10618908E+05 RMS= 0.172590E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0773E+04 1.7321E+01 1.2872E+02 C 4762 BOND = 1412.2011 ANGLE = 3708.2679 DIHED = 5450.2811 VDWAALS = -3905.2440 EEL = -35056.4120 EGB = -7755.0066 1-4 VDW = 1814.7561 1-4 EEL = 23374.0802 RESTRAINT = 0.0000 ESURF = 184.0003 minimization completed, ENE= -.10773076E+05 RMS= 0.173212E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0661E+04 1.7625E+01 1.1176E+02 CA 6043 BOND = 1457.9740 ANGLE = 3822.4309 DIHED = 5428.1804 VDWAALS = -3929.5128 EEL = -35068.1599 EGB = -7724.3005 1-4 VDW = 1792.5436 1-4 EEL = 23374.5126 RESTRAINT = 0.0000 ESURF = 185.0769 minimization completed, ENE= -.10661255E+05 RMS= 0.176248E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0756E+04 1.7450E+01 1.1386E+02 CA 3300 BOND = 1423.6734 ANGLE = 3675.3448 DIHED = 5398.3892 VDWAALS = -3912.9722 EEL = -35113.8659 EGB = -7653.2217 1-4 VDW = 1824.5441 1-4 EEL = 23419.7507 RESTRAINT = 0.0000 ESURF = 182.4151 minimization completed, ENE= -.10755942E+05 RMS= 0.174503E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0684E+04 1.7456E+01 1.0469E+02 CG 2852 BOND = 1405.1483 ANGLE = 3753.8946 DIHED = 5460.9890 VDWAALS = -3916.9256 EEL = -35043.0276 EGB = -7709.9301 1-4 VDW = 1798.1758 1-4 EEL = 23384.1646 RESTRAINT = 0.0000 ESURF = 183.3698 minimization completed, ENE= -.10684141E+05 RMS= 0.174561E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0727E+04 1.7317E+01 1.0924E+02 C 3951 BOND = 1414.0042 ANGLE = 3691.3182 DIHED = 5449.8614 VDWAALS = -3853.2197 EEL = -35271.0129 EGB = -7579.6553 1-4 VDW = 1822.0280 1-4 EEL = 23416.8767 RESTRAINT = 0.0000 ESURF = 182.9160 minimization completed, ENE= -.10726883E+05 RMS= 0.173172E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0795E+04 1.7355E+01 1.0994E+02 CA 4320 BOND = 1418.5692 ANGLE = 3697.9719 DIHED = 5422.9802 VDWAALS = -3947.7195 EEL = -35259.1647 EGB = -7621.9962 1-4 VDW = 1804.9815 1-4 EEL = 23506.5809 RESTRAINT = 0.0000 ESURF = 182.4882 minimization completed, ENE= -.10795309E+05 RMS= 0.173551E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0771E+04 1.7408E+01 1.2433E+02 C 4859 BOND = 1425.8648 ANGLE = 3768.8363 DIHED = 5384.9503 VDWAALS = -3930.0446 EEL = -35097.6856 EGB = -7654.1019 1-4 VDW = 1791.6513 1-4 EEL = 23358.5022 RESTRAINT = 0.0000 ESURF = 181.0562 minimization completed, ENE= -.10770971E+05 RMS= 0.174085E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0744E+04 1.7454E+01 1.3368E+02 C 6097 BOND = 1427.9188 ANGLE = 3699.1683 DIHED = 5461.9298 VDWAALS = -3903.4930 EEL = -34987.8946 EGB = -7749.7905 1-4 VDW = 1787.2781 1-4 EEL = 23337.5025 RESTRAINT = 0.0000 ESURF = 183.2971 minimization completed, ENE= -.10744083E+05 RMS= 0.174545E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0802E+04 1.7338E+01 1.1211E+02 CZ 4801 BOND = 1407.7518 ANGLE = 3763.0717 DIHED = 5444.9763 VDWAALS = -3982.2995 EEL = -35034.8527 EGB = -7735.6007 1-4 VDW = 1779.5664 1-4 EEL = 23372.5832 RESTRAINT = 0.0000 ESURF = 182.3099 minimization completed, ENE= -.10802494E+05 RMS= 0.173382E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0724E+04 1.7323E+01 1.0910E+02 C 2514 BOND = 1417.1051 ANGLE = 3699.8730 DIHED = 5443.3607 VDWAALS = -3907.0378 EEL = -35115.0054 EGB = -7622.5028 1-4 VDW = 1821.0323 1-4 EEL = 23357.2390 RESTRAINT = 0.0000 ESURF = 181.7375 minimization completed, ENE= -.10724198E+05 RMS= 0.173235E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0807E+04 1.7235E+01 1.0636E+02 PG 7838 BOND = 1400.2688 ANGLE = 3715.7022 DIHED = 5399.5967 VDWAALS = -3917.7474 EEL = -35043.3360 EGB = -7719.9859 1-4 VDW = 1789.6843 1-4 EEL = 23388.0560 RESTRAINT = 0.0000 ESURF = 181.2131 minimization completed, ENE= -.10806548E+05 RMS= 0.172346E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0796E+04 1.7283E+01 1.2443E+02 CE 413 BOND = 1392.5350 ANGLE = 3713.6715 DIHED = 5444.9545 VDWAALS = -3902.2185 EEL = -34995.9119 EGB = -7751.3949 1-4 VDW = 1802.6901 1-4 EEL = 23316.4254 RESTRAINT = 0.0000 ESURF = 182.9731 minimization completed, ENE= -.10796276E+05 RMS= 0.172833E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0724E+04 1.7426E+01 1.2573E+02 C 2951 BOND = 1417.9712 ANGLE = 3735.9606 DIHED = 5427.3868 VDWAALS = -3906.9463 EEL = -35072.2761 EGB = -7692.8890 1-4 VDW = 1821.3140 1-4 EEL = 23363.3257 RESTRAINT = 0.0000 ESURF = 182.3097 minimization completed, ENE= -.10723843E+05 RMS= 0.174258E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0706E+04 1.7118E+01 1.0964E+02 C 4824 BOND = 1417.5078 ANGLE = 3810.8053 DIHED = 5407.6493 VDWAALS = -3890.2552 EEL = -35299.6356 EGB = -7562.5448 1-4 VDW = 1833.0391 1-4 EEL = 23395.4929 RESTRAINT = 0.0000 ESURF = 181.5347 minimization completed, ENE= -.10706407E+05 RMS= 0.171179E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0694E+04 1.7157E+01 1.0790E+02 CD 6494 BOND = 1417.9537 ANGLE = 3740.2181 DIHED = 5431.7277 VDWAALS = -3871.5265 EEL = -35068.4617 EGB = -7713.6758 1-4 VDW = 1816.4251 1-4 EEL = 23368.1726 RESTRAINT = 0.0000 ESURF = 184.9144 minimization completed, ENE= -.10694252E+05 RMS= 0.171567E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0677E+04 1.7682E+01 1.1795E+02 NE 534 BOND = 1440.3553 ANGLE = 3770.5617 DIHED = 5405.8330 VDWAALS = -3860.9007 EEL = -35137.4338 EGB = -7698.4709 1-4 VDW = 1847.4832 1-4 EEL = 23371.0049 RESTRAINT = 0.0000 ESURF = 184.2342 minimization completed, ENE= -.10677333E+05 RMS= 0.176820E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0750E+04 1.7348E+01 1.0652E+02 CA 5602 BOND = 1363.5809 ANGLE = 3742.6052 DIHED = 5443.5841 VDWAALS = -3874.3075 EEL = -35016.1798 EGB = -7764.1485 1-4 VDW = 1817.7554 1-4 EEL = 23355.1902 RESTRAINT = 0.0000 ESURF = 182.1867 minimization completed, ENE= -.10749733E+05 RMS= 0.173483E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0783E+04 1.7375E+01 1.2435E+02 CD 3539 BOND = 1416.9167 ANGLE = 3735.7132 DIHED = 5393.1992 VDWAALS = -3915.7559 EEL = -34841.8303 EGB = -7840.4566 1-4 VDW = 1808.2083 1-4 EEL = 23278.3602 RESTRAINT = 0.0000 ESURF = 182.7457 minimization completed, ENE= -.10782900E+05 RMS= 0.173750E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0812E+04 1.7237E+01 1.2562E+02 CD 6463 BOND = 1384.2811 ANGLE = 3683.8723 DIHED = 5415.6418 VDWAALS = -3883.4443 EEL = -35019.1847 EGB = -7779.9792 1-4 VDW = 1828.3925 1-4 EEL = 23374.3509 RESTRAINT = 0.0000 ESURF = 184.2235 minimization completed, ENE= -.10811846E+05 RMS= 0.172372E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0715E+04 1.7388E+01 1.1750E+02 CG 1287 BOND = 1452.4666 ANGLE = 3689.9907 DIHED = 5464.9601 VDWAALS = -3884.0980 EEL = -35093.4488 EGB = -7656.7426 1-4 VDW = 1807.7198 1-4 EEL = 23321.3849 RESTRAINT = 0.0000 ESURF = 183.2350 minimization completed, ENE= -.10714532E+05 RMS= 0.173881E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0649E+04 1.7360E+01 1.0699E+02 CA 796 BOND = 1431.2859 ANGLE = 3783.7182 DIHED = 5482.8268 VDWAALS = -3915.7234 EEL = -35009.5605 EGB = -7703.3485 1-4 VDW = 1813.9225 1-4 EEL = 23285.1240 RESTRAINT = 0.0000 ESURF = 182.6347 minimization completed, ENE= -.10649120E+05 RMS= 0.173598E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0686E+04 1.7450E+01 1.1660E+02 CG 4706 BOND = 1454.9498 ANGLE = 3714.7789 DIHED = 5464.0589 VDWAALS = -3927.1059 EEL = -35046.3166 EGB = -7704.6114 1-4 VDW = 1789.4451 1-4 EEL = 23387.1282 RESTRAINT = 0.0000 ESURF = 181.3112 minimization completed, ENE= -.10686362E+05 RMS= 0.174498E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0785E+04 1.7372E+01 1.1215E+02 CD 4694 BOND = 1406.0123 ANGLE = 3709.0158 DIHED = 5434.4979 VDWAALS = -3934.0251 EEL = -35038.7709 EGB = -7711.1944 1-4 VDW = 1804.1863 1-4 EEL = 23362.3223 RESTRAINT = 0.0000 ESURF = 183.4464 minimization completed, ENE= -.10784509E+05 RMS= 0.173724E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0682E+04 1.7491E+01 1.1606E+02 N 4711 BOND = 1455.0750 ANGLE = 3716.7861 DIHED = 5438.4260 VDWAALS = -3904.8530 EEL = -34901.4429 EGB = -7798.0900 1-4 VDW = 1787.4719 1-4 EEL = 23342.2163 RESTRAINT = 0.0000 ESURF = 181.9765 minimization completed, ENE= -.10682434E+05 RMS= 0.174913E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0855E+04 1.6901E+01 1.1846E+02 C 3011 BOND = 1369.8832 ANGLE = 3692.7671 DIHED = 5383.6638 VDWAALS = -3881.8680 EEL = -35094.9306 EGB = -7581.6301 1-4 VDW = 1771.8859 1-4 EEL = 23301.5786 RESTRAINT = 0.0000 ESURF = 184.0357 minimization completed, ENE= -.10854614E+05 RMS= 0.169010E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0642E+04 1.7590E+01 1.3094E+02 N 5827 BOND = 1488.9785 ANGLE = 3685.8524 DIHED = 5422.0475 VDWAALS = -3878.3286 EEL = -34886.5966 EGB = -7741.2387 1-4 VDW = 1805.4207 1-4 EEL = 23278.2713 RESTRAINT = 0.0000 ESURF = 183.6459 minimization completed, ENE= -.10641948E+05 RMS= 0.175903E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0687E+04 1.7590E+01 1.2187E+02 C 6739 BOND = 1459.1501 ANGLE = 3640.3129 DIHED = 5473.0280 VDWAALS = -3904.8768 EEL = -34985.2312 EGB = -7735.1408 1-4 VDW = 1817.1621 1-4 EEL = 23364.7949 RESTRAINT = 0.0000 ESURF = 183.6757 minimization completed, ENE= -.10687125E+05 RMS= 0.175899E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0775E+04 1.7535E+01 1.4858E+02 CD 2701 BOND = 1466.1590 ANGLE = 3697.3022 DIHED = 5401.7326 VDWAALS = -3932.7885 EEL = -34953.8848 EGB = -7760.4320 1-4 VDW = 1810.0318 1-4 EEL = 23314.8366 RESTRAINT = 0.0000 ESURF = 182.1526 minimization completed, ENE= -.10774890E+05 RMS= 0.175346E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0674E+04 1.7347E+01 1.1052E+02 C 1225 BOND = 1392.2702 ANGLE = 3779.7890 DIHED = 5439.3743 VDWAALS = -3923.9310 EEL = -35146.9638 EGB = -7602.7453 1-4 VDW = 1819.0837 1-4 EEL = 23387.2063 RESTRAINT = 0.0000 ESURF = 181.6782 minimization completed, ENE= -.10674238E+05 RMS= 0.173468E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0764E+04 1.6991E+01 1.1459E+02 C 3653 BOND = 1392.4865 ANGLE = 3735.0305 DIHED = 5441.9067 VDWAALS = -3958.1188 EEL = -35038.2354 EGB = -7721.6911 1-4 VDW = 1831.5541 1-4 EEL = 23371.3797 RESTRAINT = 0.0000 ESURF = 181.7867 minimization completed, ENE= -.10763901E+05 RMS= 0.169906E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0639E+04 1.7621E+01 1.1482E+02 CG 244 BOND = 1446.7242 ANGLE = 3792.6664 DIHED = 5451.0536 VDWAALS = -3914.4515 EEL = -34987.9907 EGB = -7716.1809 1-4 VDW = 1801.5866 1-4 EEL = 23303.9395 RESTRAINT = 0.0000 ESURF = 183.5307 minimization completed, ENE= -.10639122E+05 RMS= 0.176212E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0840E+04 1.6932E+01 1.1264E+02 C 4018 BOND = 1377.9870 ANGLE = 3664.9177 DIHED = 5436.2988 VDWAALS = -3892.5812 EEL = -35100.4313 EGB = -7692.4035 1-4 VDW = 1817.7718 1-4 EEL = 23365.5579 RESTRAINT = 0.0000 ESURF = 182.6283 minimization completed, ENE= -.10840255E+05 RMS= 0.169319E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0711E+04 1.7416E+01 1.0784E+02 C 2041 BOND = 1393.4075 ANGLE = 3738.9101 DIHED = 5383.7456 VDWAALS = -3937.7682 EEL = -35033.9415 EGB = -7645.8994 1-4 VDW = 1841.3856 1-4 EEL = 23367.7580 RESTRAINT = 0.0000 ESURF = 181.6519 minimization completed, ENE= -.10710750E+05 RMS= 0.174157E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0789E+04 1.7200E+01 1.4114E+02 CD 4614 BOND = 1423.5751 ANGLE = 3761.9495 DIHED = 5439.4342 VDWAALS = -3935.0181 EEL = -34988.6220 EGB = -7767.2677 1-4 VDW = 1788.1200 1-4 EEL = 23307.2791 RESTRAINT = 0.0000 ESURF = 182.0313 minimization completed, ENE= -.10788519E+05 RMS= 0.172002E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0746E+04 1.7341E+01 1.2701E+02 CD 6521 BOND = 1412.1238 ANGLE = 3700.3239 DIHED = 5420.6968 VDWAALS = -3844.5022 EEL = -34940.9803 EGB = -7804.6234 1-4 VDW = 1798.4425 1-4 EEL = 23327.7091 RESTRAINT = 0.0000 ESURF = 185.2351 minimization completed, ENE= -.10745575E+05 RMS= 0.173414E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0735E+04 1.7298E+01 1.0734E+02 C 2271 BOND = 1420.1205 ANGLE = 3654.4655 DIHED = 5442.3341 VDWAALS = -3920.2959 EEL = -34840.6589 EGB = -7849.0963 1-4 VDW = 1819.5549 1-4 EEL = 23353.0432 RESTRAINT = 0.0000 ESURF = 185.2173 minimization completed, ENE= -.10735315E+05 RMS= 0.172979E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0817E+04 1.7090E+01 1.0062E+02 C 2767 BOND = 1400.8260 ANGLE = 3690.1721 DIHED = 5436.4626 VDWAALS = -3848.8522 EEL = -35079.6243 EGB = -7715.7978 1-4 VDW = 1803.5060 1-4 EEL = 23310.3981 RESTRAINT = 0.0000 ESURF = 185.6195 minimization completed, ENE= -.10817290E+05 RMS= 0.170901E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0736E+04 1.7311E+01 1.0869E+02 C 4735 BOND = 1393.1859 ANGLE = 3763.5880 DIHED = 5467.1072 VDWAALS = -3832.8028 EEL = -35175.6582 EGB = -7636.6084 1-4 VDW = 1799.0690 1-4 EEL = 23301.0408 RESTRAINT = 0.0000 ESURF = 185.5121 minimization completed, ENE= -.10735566E+05 RMS= 0.173108E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0676E+04 1.7155E+01 1.0123E+02 C 7074 BOND = 1394.1352 ANGLE = 3746.7144 DIHED = 5458.4513 VDWAALS = -3860.9775 EEL = -35085.0717 EGB = -7631.2440 1-4 VDW = 1820.0377 1-4 EEL = 23296.5324 RESTRAINT = 0.0000 ESURF = 185.5107 minimization completed, ENE= -.10675911E+05 RMS= 0.171550E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 677.57 ( 7.53% of Gen B) | Calc gb diag 5332.00 (59.22% of Gen B) | Calc gb off-diag 2994.02 (33.25% of Gen B) | Gen Born time 9003.59 (100.0% of Nonbo) | Nonbond force 9003.59 (100.0% of Force) | Bond/Angle/Dihedral 7.06 ( 0.08% of Force) | Force time 9010.66 (100.0% of Runmd) | Runmd Time 9010.66 (98.97% of Total) | Other 93.72 ( 1.03% of Total) | Total time 9104.40 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 00:30:16.470 on 10/20/2010 | Setup done at 00:30:17.437 on 10/20/2010 | Run done at 03:02:00.870 on 10/20/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/20/2010 at 00:30:16 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _lig.out.5 |INPCRD: 1XCK_chainA_MGATP_noWAT.inpcrd | PARM: 1XCK_chainA_MGATP_noWAT.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _lig.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 = 09/24/09 Time = 02:43:23 NATOM = 7879 NTYPES = 18 NBONH = 3991 MBONA = 3917 NTHETH = 9115 MTHETA = 5297 NPHIH = 17023 MPHIA = 12427 NHPARM = 0 NPARM = 0 NNB = 43422 NRES = 526 NBONA = 3917 NTHETA = 5297 NPHIA = 12427 NUMBND = 52 NUMANG = 108 NPTRA = 66 NATYP = 36 NPHB = 0 IFBOX = 0 NMXRS = 43 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 567848 | Hollerith 24165 | Integer 1061772 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 8678 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 -1.0643E+04 1.7291E+01 1.0579E+02 N 2472 BOND = 1437.4530 ANGLE = 3765.5131 DIHED = 5425.5434 VDWAALS = -3921.7782 EEL = -34559.8041 EGB = -8069.8456 1-4 VDW = 1806.4248 1-4 EEL = 23287.4995 RESTRAINT = 0.0000 ESURF = 185.5256 minimization completed, ENE= -.10643468E+05 RMS= 0.172914E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0641E+04 1.7287E+01 1.1624E+02 PG 7838 BOND = 1388.4915 ANGLE = 3783.6713 DIHED = 5414.4181 VDWAALS = -3866.7937 EEL = -34792.6084 EGB = -7909.9808 1-4 VDW = 1817.1908 1-4 EEL = 23340.7972 RESTRAINT = 0.0000 ESURF = 183.8302 minimization completed, ENE= -.10640984E+05 RMS= 0.172868E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0762E+04 1.7268E+01 1.0593E+02 CD 2137 BOND = 1429.9784 ANGLE = 3715.4265 DIHED = 5426.2200 VDWAALS = -3959.0952 EEL = -34737.2943 EGB = -7929.9270 1-4 VDW = 1784.9572 1-4 EEL = 23323.5578 RESTRAINT = 0.0000 ESURF = 184.0311 minimization completed, ENE= -.10762145E+05 RMS= 0.172677E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0633E+04 1.7564E+01 1.1222E+02 C 4663 BOND = 1434.7431 ANGLE = 3731.6905 DIHED = 5439.4135 VDWAALS = -3915.8744 EEL = -34850.7874 EGB = -7897.3442 1-4 VDW = 1830.8152 1-4 EEL = 23411.9742 RESTRAINT = 0.0000 ESURF = 182.3382 minimization completed, ENE= -.10633031E+05 RMS= 0.175644E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0789E+04 1.7383E+01 1.2539E+02 N 4619 BOND = 1423.8608 ANGLE = 3707.1741 DIHED = 5391.3693 VDWAALS = -3904.5217 EEL = -34760.8261 EGB = -7974.5002 1-4 VDW = 1791.9161 1-4 EEL = 23352.5530 RESTRAINT = 0.0000 ESURF = 183.7678 minimization completed, ENE= -.10789207E+05 RMS= 0.173832E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0707E+04 1.7440E+01 1.2076E+02 CA 3911 BOND = 1486.8787 ANGLE = 3677.0667 DIHED = 5436.9921 VDWAALS = -3902.4320 EEL = -34737.0119 EGB = -8045.8115 1-4 VDW = 1807.6843 1-4 EEL = 23385.4387 RESTRAINT = 0.0000 ESURF = 184.6519 minimization completed, ENE= -.10706543E+05 RMS= 0.174405E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0778E+04 1.7297E+01 1.1009E+02 C 2179 BOND = 1447.1347 ANGLE = 3735.2104 DIHED = 5419.6114 VDWAALS = -3871.6501 EEL = -35038.2717 EGB = -7854.9598 1-4 VDW = 1807.4252 1-4 EEL = 23395.9106 RESTRAINT = 0.0000 ESURF = 182.0228 minimization completed, ENE= -.10777566E+05 RMS= 0.172966E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0822E+04 1.7172E+01 1.2217E+02 C 113 BOND = 1399.3380 ANGLE = 3714.1855 DIHED = 5412.1528 VDWAALS = -3939.3002 EEL = -34823.0353 EGB = -7932.1174 1-4 VDW = 1789.3466 1-4 EEL = 23374.7408 RESTRAINT = 0.0000 ESURF = 182.3912 minimization completed, ENE= -.10822298E+05 RMS= 0.171722E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0677E+04 1.7435E+01 1.0696E+02 OE1 4523 BOND = 1454.9872 ANGLE = 3743.5099 DIHED = 5409.7221 VDWAALS = -3976.7478 EEL = -34690.6761 EGB = -7905.0528 1-4 VDW = 1808.5184 1-4 EEL = 23297.6127 RESTRAINT = 0.0000 ESURF = 180.7496 minimization completed, ENE= -.10677377E+05 RMS= 0.174351E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0712E+04 1.7333E+01 1.0039E+02 CB 779 BOND = 1434.0589 ANGLE = 3719.9044 DIHED = 5436.3039 VDWAALS = -3916.4241 EEL = -34676.2964 EGB = -8004.2578 1-4 VDW = 1788.6292 1-4 EEL = 23325.4440 RESTRAINT = 0.0000 ESURF = 180.8380 minimization completed, ENE= -.10711800E+05 RMS= 0.173334E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0773E+04 1.7197E+01 1.2000E+02 CB 5890 BOND = 1447.3496 ANGLE = 3727.5042 DIHED = 5409.0545 VDWAALS = -3920.7733 EEL = -34793.5572 EGB = -7941.5121 1-4 VDW = 1804.7567 1-4 EEL = 23310.0966 RESTRAINT = 0.0000 ESURF = 183.9497 minimization completed, ENE= -.10773131E+05 RMS= 0.171971E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0695E+04 1.7352E+01 1.3213E+02 C 2064 BOND = 1422.9863 ANGLE = 3790.0709 DIHED = 5400.2751 VDWAALS = -3907.4826 EEL = -34857.2335 EGB = -7955.2462 1-4 VDW = 1787.6518 1-4 EEL = 23438.1516 RESTRAINT = 0.0000 ESURF = 185.5568 minimization completed, ENE= -.10695270E+05 RMS= 0.173516E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0637E+04 1.7567E+01 1.3543E+02 CG 5359 BOND = 1431.4086 ANGLE = 3772.8713 DIHED = 5449.8256 VDWAALS = -3885.7846 EEL = -35082.8056 EGB = -7750.6412 1-4 VDW = 1822.9172 1-4 EEL = 23421.8761 RESTRAINT = 0.0000 ESURF = 183.1965 minimization completed, ENE= -.10637136E+05 RMS= 0.175674E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0689E+04 1.7287E+01 1.1180E+02 CA 2305 BOND = 1370.5012 ANGLE = 3777.9750 DIHED = 5383.0302 VDWAALS = -3860.2740 EEL = -34907.7029 EGB = -7854.3921 1-4 VDW = 1819.3426 1-4 EEL = 23399.0165 RESTRAINT = 0.0000 ESURF = 183.9936 minimization completed, ENE= -.10688510E+05 RMS= 0.172868E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0810E+04 1.7402E+01 1.1766E+02 C 5098 BOND = 1419.5289 ANGLE = 3693.8065 DIHED = 5431.0510 VDWAALS = -3918.9662 EEL = -34974.4176 EGB = -7826.1500 1-4 VDW = 1794.3134 1-4 EEL = 23387.7858 RESTRAINT = 0.0000 ESURF = 182.7604 minimization completed, ENE= -.10810288E+05 RMS= 0.174017E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0800E+04 1.7042E+01 1.2381E+02 NZ 4052 BOND = 1317.0021 ANGLE = 3782.8822 DIHED = 5401.0979 VDWAALS = -3919.2041 EEL = -34948.6325 EGB = -7879.0879 1-4 VDW = 1817.7618 1-4 EEL = 23444.6105 RESTRAINT = 0.0000 ESURF = 183.9452 minimization completed, ENE= -.10799625E+05 RMS= 0.170421E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0830E+04 1.6941E+01 1.1190E+02 CG 2610 BOND = 1401.0196 ANGLE = 3613.4875 DIHED = 5376.0673 VDWAALS = -3916.7926 EEL = -34775.8791 EGB = -7828.2611 1-4 VDW = 1815.1397 1-4 EEL = 23302.8194 RESTRAINT = 0.0000 ESURF = 182.4044 minimization completed, ENE= -.10829995E+05 RMS= 0.169413E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0799E+04 1.7262E+01 1.0734E+02 C 1528 BOND = 1427.2641 ANGLE = 3705.7339 DIHED = 5401.6617 VDWAALS = -3922.2739 EEL = -34776.8535 EGB = -7953.0023 1-4 VDW = 1779.6777 1-4 EEL = 23354.2076 RESTRAINT = 0.0000 ESURF = 184.7149 minimization completed, ENE= -.10798870E+05 RMS= 0.172625E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0736E+04 1.7285E+01 1.1822E+02 C 4316 BOND = 1410.9488 ANGLE = 3684.7275 DIHED = 5440.8037 VDWAALS = -3912.7591 EEL = -34715.8460 EGB = -7975.5154 1-4 VDW = 1818.8509 1-4 EEL = 23331.0764 RESTRAINT = 0.0000 ESURF = 181.9595 minimization completed, ENE= -.10735754E+05 RMS= 0.172851E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0798E+04 1.7290E+01 1.2260E+02 C 3848 BOND = 1422.2605 ANGLE = 3663.2591 DIHED = 5373.0227 VDWAALS = -3920.7682 EEL = -34662.8669 EGB = -8002.9623 1-4 VDW = 1811.2291 1-4 EEL = 23334.8307 RESTRAINT = 0.0000 ESURF = 184.1313 minimization completed, ENE= -.10797864E+05 RMS= 0.172895E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0759E+04 1.7107E+01 1.2764E+02 CG 4342 BOND = 1370.5173 ANGLE = 3752.2668 DIHED = 5388.2180 VDWAALS = -3886.0748 EEL = -34795.0752 EGB = -7946.8832 1-4 VDW = 1800.5484 1-4 EEL = 23372.3223 RESTRAINT = 0.0000 ESURF = 185.4120 minimization completed, ENE= -.10758748E+05 RMS= 0.171067E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0753E+04 1.7456E+01 1.1205E+02 CB 4955 BOND = 1416.3959 ANGLE = 3780.5516 DIHED = 5357.5281 VDWAALS = -3903.5265 EEL = -34867.7537 EGB = -7788.4103 1-4 VDW = 1797.5105 1-4 EEL = 23272.3272 RESTRAINT = 0.0000 ESURF = 182.1872 minimization completed, ENE= -.10753190E+05 RMS= 0.174558E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0771E+04 1.7344E+01 1.0920E+02 C 2735 BOND = 1420.3199 ANGLE = 3696.3083 DIHED = 5413.3561 VDWAALS = -3884.3221 EEL = -35022.7242 EGB = -7784.0931 1-4 VDW = 1794.7395 1-4 EEL = 23411.0452 RESTRAINT = 0.0000 ESURF = 184.6701 minimization completed, ENE= -.10770700E+05 RMS= 0.173443E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0711E+04 1.7322E+01 1.3441E+02 CD2 2970 BOND = 1396.4777 ANGLE = 3766.4565 DIHED = 5404.2873 VDWAALS = -3933.7622 EEL = -34802.6435 EGB = -7856.4243 1-4 VDW = 1792.2488 1-4 EEL = 23338.3690 RESTRAINT = 0.0000 ESURF = 183.8587 minimization completed, ENE= -.10711132E+05 RMS= 0.173218E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0725E+04 1.7274E+01 1.0593E+02 CA 7831 BOND = 1417.5051 ANGLE = 3670.9773 DIHED = 5425.0614 VDWAALS = -3935.9914 EEL = -34877.3775 EGB = -7767.7370 1-4 VDW = 1819.6192 1-4 EEL = 23339.3790 RESTRAINT = 0.0000 ESURF = 183.2625 minimization completed, ENE= -.10725301E+05 RMS= 0.172739E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0745E+04 1.7447E+01 1.0475E+02 C 869 BOND = 1416.6514 ANGLE = 3728.3159 DIHED = 5438.1359 VDWAALS = -3921.3939 EEL = -34969.7143 EGB = -7863.8366 1-4 VDW = 1825.7277 1-4 EEL = 23415.7912 RESTRAINT = 0.0000 ESURF = 184.9041 minimization completed, ENE= -.10745419E+05 RMS= 0.174470E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0693E+04 1.7272E+01 1.1245E+02 C 7026 BOND = 1415.5142 ANGLE = 3723.9281 DIHED = 5448.6431 VDWAALS = -3888.7200 EEL = -34874.9158 EGB = -7808.0820 1-4 VDW = 1812.5393 1-4 EEL = 23292.4838 RESTRAINT = 0.0000 ESURF = 185.3773 minimization completed, ENE= -.10693232E+05 RMS= 0.172721E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0756E+04 1.7068E+01 1.0272E+02 CG 5392 BOND = 1405.9864 ANGLE = 3730.5286 DIHED = 5402.7085 VDWAALS = -3888.6744 EEL = -34715.5522 EGB = -7977.5256 1-4 VDW = 1808.4452 1-4 EEL = 23293.2448 RESTRAINT = 0.0000 ESURF = 184.9288 minimization completed, ENE= -.10755910E+05 RMS= 0.170675E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0670E+04 1.7482E+01 1.2296E+02 C 2233 BOND = 1460.3663 ANGLE = 3807.7191 DIHED = 5394.4161 VDWAALS = -3886.6871 EEL = -34912.0325 EGB = -7837.6265 1-4 VDW = 1791.3446 1-4 EEL = 23325.3440 RESTRAINT = 0.0000 ESURF = 186.6615 minimization completed, ENE= -.10670495E+05 RMS= 0.174823E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0791E+04 1.7554E+01 1.2998E+02 C 2368 BOND = 1460.4341 ANGLE = 3706.8179 DIHED = 5391.3978 VDWAALS = -3860.4841 EEL = -35025.1587 EGB = -7743.9560 1-4 VDW = 1792.2453 1-4 EEL = 23302.8767 RESTRAINT = 0.0000 ESURF = 185.1120 minimization completed, ENE= -.10790715E+05 RMS= 0.175543E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0716E+04 1.7436E+01 1.2763E+02 C 5638 BOND = 1479.3832 ANGLE = 3682.6211 DIHED = 5411.3959 VDWAALS = -3930.5800 EEL = -35004.5308 EGB = -7713.2013 1-4 VDW = 1824.0049 1-4 EEL = 23351.3653 RESTRAINT = 0.0000 ESURF = 183.7100 minimization completed, ENE= -.10715832E+05 RMS= 0.174358E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0822E+04 1.7551E+01 1.0928E+02 C 7615 BOND = 1453.4629 ANGLE = 3669.8631 DIHED = 5409.8342 VDWAALS = -3983.5559 EEL = -34823.0315 EGB = -7808.8590 1-4 VDW = 1792.5911 1-4 EEL = 23284.8842 RESTRAINT = 0.0000 ESURF = 182.5550 minimization completed, ENE= -.10822256E+05 RMS= 0.175510E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0755E+04 1.7296E+01 1.1970E+02 C 4495 BOND = 1413.4681 ANGLE = 3758.4627 DIHED = 5383.1154 VDWAALS = -3936.1182 EEL = -35069.6895 EGB = -7677.0151 1-4 VDW = 1830.1302 1-4 EEL = 23360.2211 RESTRAINT = 0.0000 ESURF = 182.1188 minimization completed, ENE= -.10755307E+05 RMS= 0.172961E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0888E+04 1.7047E+01 1.3353E+02 C 6444 BOND = 1330.4556 ANGLE = 3687.7446 DIHED = 5397.3570 VDWAALS = -3908.3414 EEL = -34960.8087 EGB = -7793.6757 1-4 VDW = 1815.6328 1-4 EEL = 23359.4309 RESTRAINT = 0.0000 ESURF = 183.7750 minimization completed, ENE= -.10888430E+05 RMS= 0.170466E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0753E+04 1.7294E+01 1.1760E+02 C 3492 BOND = 1407.9447 ANGLE = 3684.8992 DIHED = 5415.4484 VDWAALS = -3871.7028 EEL = -35010.4441 EGB = -7710.1320 1-4 VDW = 1823.2246 1-4 EEL = 23323.0971 RESTRAINT = 0.0000 ESURF = 184.6101 minimization completed, ENE= -.10753055E+05 RMS= 0.172941E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0817E+04 1.7213E+01 1.2293E+02 CA 7719 BOND = 1406.2638 ANGLE = 3754.2713 DIHED = 5395.5914 VDWAALS = -3961.7412 EEL = -35044.9955 EGB = -7730.5303 1-4 VDW = 1806.6584 1-4 EEL = 23371.9799 RESTRAINT = 0.0000 ESURF = 185.4248 minimization completed, ENE= -.10817077E+05 RMS= 0.172129E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0837E+04 1.7056E+01 1.0609E+02 C 2125 BOND = 1376.2672 ANGLE = 3730.6294 DIHED = 5385.9426 VDWAALS = -3926.2211 EEL = -34968.3233 EGB = -7738.0709 1-4 VDW = 1805.4523 1-4 EEL = 23313.7886 RESTRAINT = 0.0000 ESURF = 183.9996 minimization completed, ENE= -.10836536E+05 RMS= 0.170556E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0726E+04 1.7583E+01 1.1317E+02 C 3829 BOND = 1383.1839 ANGLE = 3742.0573 DIHED = 5430.5452 VDWAALS = -3912.9800 EEL = -35143.7149 EGB = -7729.9640 1-4 VDW = 1850.0988 1-4 EEL = 23471.2615 RESTRAINT = 0.0000 ESURF = 183.6601 minimization completed, ENE= -.10725852E+05 RMS= 0.175831E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0697E+04 1.7436E+01 1.1130E+02 C 55 BOND = 1376.1713 ANGLE = 3713.0492 DIHED = 5487.9077 VDWAALS = -3913.5649 EEL = -34967.1981 EGB = -7708.4171 1-4 VDW = 1808.7902 1-4 EEL = 23323.1572 RESTRAINT = 0.0000 ESURF = 183.1709 minimization completed, ENE= -.10696934E+05 RMS= 0.174359E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0818E+04 1.7138E+01 1.3504E+02 CD 5774 BOND = 1396.8514 ANGLE = 3657.6957 DIHED = 5398.2340 VDWAALS = -3941.5841 EEL = -34966.7121 EGB = -7747.5705 1-4 VDW = 1810.1703 1-4 EEL = 23391.8720 RESTRAINT = 0.0000 ESURF = 183.2743 minimization completed, ENE= -.10817769E+05 RMS= 0.171378E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0720E+04 1.7348E+01 1.0053E+02 C 4421 BOND = 1417.6041 ANGLE = 3699.2394 DIHED = 5448.7574 VDWAALS = -3890.8674 EEL = -34876.3419 EGB = -7856.6621 1-4 VDW = 1809.2206 1-4 EEL = 23346.8036 RESTRAINT = 0.0000 ESURF = 182.6552 minimization completed, ENE= -.10719591E+05 RMS= 0.173476E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0711E+04 1.7457E+01 1.1721E+02 C 952 BOND = 1475.9840 ANGLE = 3666.1950 DIHED = 5382.2349 VDWAALS = -3830.3265 EEL = -34940.9028 EGB = -7818.9098 1-4 VDW = 1794.2621 1-4 EEL = 23374.6679 RESTRAINT = 0.0000 ESURF = 185.3652 minimization completed, ENE= -.10711430E+05 RMS= 0.174572E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0722E+04 1.7320E+01 1.0987E+02 CD 3816 BOND = 1434.7489 ANGLE = 3709.9267 DIHED = 5433.6997 VDWAALS = -3907.7030 EEL = -34951.0696 EGB = -7790.1556 1-4 VDW = 1790.2029 1-4 EEL = 23373.4908 RESTRAINT = 0.0000 ESURF = 184.8565 minimization completed, ENE= -.10722003E+05 RMS= 0.173200E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0635E+04 1.7344E+01 1.0451E+02 CA 7211 BOND = 1459.5394 ANGLE = 3809.3961 DIHED = 5427.9201 VDWAALS = -3879.6747 EEL = -35040.8698 EGB = -7714.9238 1-4 VDW = 1794.0663 1-4 EEL = 23326.4757 RESTRAINT = 0.0000 ESURF = 182.9464 minimization completed, ENE= -.10635124E+05 RMS= 0.173444E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0685E+04 1.7469E+01 1.3422E+02 OD1 311 BOND = 1438.0370 ANGLE = 3751.6618 DIHED = 5369.3018 VDWAALS = -3859.8129 EEL = -35076.7607 EGB = -7661.6036 1-4 VDW = 1803.2934 1-4 EEL = 23366.5853 RESTRAINT = 0.0000 ESURF = 184.4868 minimization completed, ENE= -.10684811E+05 RMS= 0.174690E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0672E+04 1.7305E+01 1.1751E+02 N 6055 BOND = 1442.0495 ANGLE = 3715.5298 DIHED = 5443.7975 VDWAALS = -3950.5076 EEL = -35001.4131 EGB = -7675.2247 1-4 VDW = 1805.1542 1-4 EEL = 23365.5281 RESTRAINT = 0.0000 ESURF = 183.4546 minimization completed, ENE= -.10671632E+05 RMS= 0.173047E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0804E+04 1.7074E+01 1.1156E+02 C 6940 BOND = 1390.2681 ANGLE = 3699.9604 DIHED = 5425.0183 VDWAALS = -3884.9411 EEL = -35066.5591 EGB = -7692.7443 1-4 VDW = 1794.0051 1-4 EEL = 23347.3380 RESTRAINT = 0.0000 ESURF = 183.8531 minimization completed, ENE= -.10803802E+05 RMS= 0.170737E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0764E+04 1.7270E+01 1.1635E+02 C 372 BOND = 1416.2910 ANGLE = 3728.8907 DIHED = 5415.5669 VDWAALS = -3859.5400 EEL = -35137.0671 EGB = -7701.3034 1-4 VDW = 1795.2846 1-4 EEL = 23394.3136 RESTRAINT = 0.0000 ESURF = 183.3657 minimization completed, ENE= -.10764198E+05 RMS= 0.172702E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0659E+04 1.7397E+01 1.1622E+02 CA 1624 BOND = 1421.9189 ANGLE = 3742.3354 DIHED = 5431.1321 VDWAALS = -3849.5472 EEL = -35076.2852 EGB = -7737.3996 1-4 VDW = 1840.1802 1-4 EEL = 23383.5685 RESTRAINT = 0.0000 ESURF = 185.1596 minimization completed, ENE= -.10658937E+05 RMS= 0.173966E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0812E+04 1.7089E+01 1.1757E+02 C 6996 BOND = 1381.7674 ANGLE = 3699.9282 DIHED = 5421.8549 VDWAALS = -3850.5138 EEL = -35170.5611 EGB = -7643.5568 1-4 VDW = 1782.8459 1-4 EEL = 23382.0070 RESTRAINT = 0.0000 ESURF = 184.4331 minimization completed, ENE= -.10811795E+05 RMS= 0.170895E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 696.70 ( 7.75% of Gen B) | Calc gb diag 5342.38 (59.41% of Gen B) | Calc gb off-diag 2952.89 (32.84% of Gen B) | Gen Born time 8991.98 (100.0% of Nonbo) | Nonbond force 8991.98 (100.0% of Force) | Bond/Angle/Dihedral 6.66 ( 0.07% of Force) | Force time 8998.65 (100.0% of Runmd) | Runmd Time 8998.65 (98.98% of Total) | Other 92.30 ( 1.02% of Total) | Total time 9090.97 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 00:30:16.468 on 10/20/2010 | Setup done at 00:30:17.454 on 10/20/2010 | Run done at 03:01:47.436 on 10/20/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/20/2010 at 00:30:16 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _lig.out.4 |INPCRD: 1XCK_chainA_MGATP_noWAT.inpcrd | PARM: 1XCK_chainA_MGATP_noWAT.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _lig.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 = 09/24/09 Time = 02:43:23 NATOM = 7879 NTYPES = 18 NBONH = 3991 MBONA = 3917 NTHETH = 9115 MTHETA = 5297 NPHIH = 17023 MPHIA = 12427 NHPARM = 0 NPARM = 0 NNB = 43422 NRES = 526 NBONA = 3917 NTHETA = 5297 NPHIA = 12427 NUMBND = 52 NUMANG = 108 NPTRA = 66 NATYP = 36 NPHB = 0 IFBOX = 0 NMXRS = 43 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 567848 | Hollerith 24165 | Integer 1061772 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 8678 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 -1.0732E+04 1.7113E+01 1.0313E+02 CA 2407 BOND = 1380.0039 ANGLE = 3711.2582 DIHED = 5414.6103 VDWAALS = -3947.5248 EEL = -35118.7343 EGB = -7573.4878 1-4 VDW = 1830.6731 1-4 EEL = 23388.3902 RESTRAINT = 0.0000 ESURF = 182.3654 minimization completed, ENE= -.10732446E+05 RMS= 0.171132E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0776E+04 1.7300E+01 1.0735E+02 C 2064 BOND = 1421.7357 ANGLE = 3720.6997 DIHED = 5446.9465 VDWAALS = -3936.5110 EEL = -35029.0466 EGB = -7716.2173 1-4 VDW = 1795.8219 1-4 EEL = 23338.3436 RESTRAINT = 0.0000 ESURF = 181.9568 minimization completed, ENE= -.10776271E+05 RMS= 0.172998E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0799E+04 1.7211E+01 1.0998E+02 CG 129 BOND = 1391.1643 ANGLE = 3712.7413 DIHED = 5384.2070 VDWAALS = -3894.9186 EEL = -34981.3104 EGB = -7781.6353 1-4 VDW = 1809.2131 1-4 EEL = 23376.7507 RESTRAINT = 0.0000 ESURF = 184.9162 minimization completed, ENE= -.10798872E+05 RMS= 0.172111E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0698E+04 1.7522E+01 1.3757E+02 C 7741 BOND = 1449.3142 ANGLE = 3788.0982 DIHED = 5405.3525 VDWAALS = -3893.4923 EEL = -34980.4497 EGB = -7747.8685 1-4 VDW = 1807.9731 1-4 EEL = 23288.5080 RESTRAINT = 0.0000 ESURF = 184.6045 minimization completed, ENE= -.10697960E+05 RMS= 0.175221E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0727E+04 1.7420E+01 1.0146E+02 CG 2228 BOND = 1424.8953 ANGLE = 3731.8806 DIHED = 5423.3071 VDWAALS = -3891.1056 EEL = -35028.0684 EGB = -7706.8537 1-4 VDW = 1798.6779 1-4 EEL = 23334.6143 RESTRAINT = 0.0000 ESURF = 185.2816 minimization completed, ENE= -.10727371E+05 RMS= 0.174204E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0761E+04 1.7380E+01 1.1380E+02 CD 3073 BOND = 1443.9029 ANGLE = 3688.2236 DIHED = 5374.1086 VDWAALS = -3906.5155 EEL = -35022.0896 EGB = -7686.9088 1-4 VDW = 1810.2078 1-4 EEL = 23355.4342 RESTRAINT = 0.0000 ESURF = 183.0749 minimization completed, ENE= -.10760562E+05 RMS= 0.173804E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0813E+04 1.7318E+01 1.1834E+02 N 4347 BOND = 1432.4327 ANGLE = 3747.7287 DIHED = 5391.0935 VDWAALS = -3956.2249 EEL = -34992.8450 EGB = -7799.4106 1-4 VDW = 1800.8791 1-4 EEL = 23379.4383 RESTRAINT = 0.0000 ESURF = 184.3831 minimization completed, ENE= -.10812525E+05 RMS= 0.173180E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0746E+04 1.7351E+01 1.2234E+02 CZ 4217 BOND = 1427.3026 ANGLE = 3744.4635 DIHED = 5414.3183 VDWAALS = -3927.1761 EEL = -35010.9228 EGB = -7740.7672 1-4 VDW = 1821.7864 1-4 EEL = 23340.8828 RESTRAINT = 0.0000 ESURF = 183.6263 minimization completed, ENE= -.10746486E+05 RMS= 0.173514E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0627E+04 1.7610E+01 1.1418E+02 C 543 BOND = 1488.9328 ANGLE = 3783.3650 DIHED = 5441.3845 VDWAALS = -3921.2863 EEL = -34967.5889 EGB = -7794.7613 1-4 VDW = 1816.8457 1-4 EEL = 23342.6638 RESTRAINT = 0.0000 ESURF = 183.2060 minimization completed, ENE= -.10627239E+05 RMS= 0.176100E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0770E+04 1.7393E+01 1.0738E+02 N 4665 BOND = 1423.2158 ANGLE = 3735.7282 DIHED = 5393.2571 VDWAALS = -3977.6713 EEL = -34918.9483 EGB = -7721.6714 1-4 VDW = 1796.6463 1-4 EEL = 23316.0656 RESTRAINT = 0.0000 ESURF = 183.1922 minimization completed, ENE= -.10770186E+05 RMS= 0.173929E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0633E+04 1.7402E+01 1.2332E+02 C 4762 BOND = 1405.8789 ANGLE = 3822.0099 DIHED = 5416.8435 VDWAALS = -3900.1444 EEL = -34899.0736 EGB = -7774.7451 1-4 VDW = 1812.6692 1-4 EEL = 23299.1381 RESTRAINT = 0.0000 ESURF = 184.4382 minimization completed, ENE= -.10632986E+05 RMS= 0.174022E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0771E+04 1.7012E+01 1.1602E+02 CD 3751 BOND = 1382.7053 ANGLE = 3745.8518 DIHED = 5395.0854 VDWAALS = -3933.3082 EEL = -35113.1556 EGB = -7666.7714 1-4 VDW = 1836.0707 1-4 EEL = 23401.7080 RESTRAINT = 0.0000 ESURF = 181.1576 minimization completed, ENE= -.10770656E+05 RMS= 0.170117E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0812E+04 1.7246E+01 1.1002E+02 C 3384 BOND = 1412.9087 ANGLE = 3744.9681 DIHED = 5419.9831 VDWAALS = -3946.4426 EEL = -34965.0597 EGB = -7796.7551 1-4 VDW = 1786.1494 1-4 EEL = 23348.4970 RESTRAINT = 0.0000 ESURF = 184.2134 minimization completed, ENE= -.10811538E+05 RMS= 0.172458E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0650E+04 1.7309E+01 1.0934E+02 C 718 BOND = 1411.8968 ANGLE = 3762.0764 DIHED = 5460.0210 VDWAALS = -3820.1802 EEL = -34906.3163 EGB = -7972.1981 1-4 VDW = 1827.8829 1-4 EEL = 23401.2131 RESTRAINT = 0.0000 ESURF = 185.7921 minimization completed, ENE= -.10649812E+05 RMS= 0.173085E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0764E+04 1.7201E+01 1.0766E+02 CA 3876 BOND = 1350.1931 ANGLE = 3782.0657 DIHED = 5378.4845 VDWAALS = -3911.3372 EEL = -34954.3863 EGB = -7833.4019 1-4 VDW = 1822.1527 1-4 EEL = 23416.9892 RESTRAINT = 0.0000 ESURF = 185.2961 minimization completed, ENE= -.10763944E+05 RMS= 0.172009E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0751E+04 1.7515E+01 1.3974E+02 C 5728 BOND = 1441.7351 ANGLE = 3707.6462 DIHED = 5410.0942 VDWAALS = -3860.1735 EEL = -34820.7129 EGB = -7920.0143 1-4 VDW = 1803.5317 1-4 EEL = 23299.8925 RESTRAINT = 0.0000 ESURF = 187.2476 minimization completed, ENE= -.10750753E+05 RMS= 0.175152E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0651E+04 1.7366E+01 1.1776E+02 C 2601 BOND = 1413.1100 ANGLE = 3836.7235 DIHED = 5422.1571 VDWAALS = -3897.2374 EEL = -34703.9780 EGB = -8028.8475 1-4 VDW = 1804.8397 1-4 EEL = 23312.7087 RESTRAINT = 0.0000 ESURF = 189.1380 minimization completed, ENE= -.10651386E+05 RMS= 0.173660E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0731E+04 1.7163E+01 9.9715E+01 CD 7542 BOND = 1413.9306 ANGLE = 3712.6189 DIHED = 5418.5824 VDWAALS = -3916.7356 EEL = -34717.2284 EGB = -8022.4349 1-4 VDW = 1816.7706 1-4 EEL = 23376.9840 RESTRAINT = 0.0000 ESURF = 186.0782 minimization completed, ENE= -.10731434E+05 RMS= 0.171629E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0789E+04 1.7321E+01 1.1576E+02 C 6972 BOND = 1408.6026 ANGLE = 3689.9387 DIHED = 5388.2643 VDWAALS = -3884.3678 EEL = -34681.0377 EGB = -8048.8624 1-4 VDW = 1794.5983 1-4 EEL = 23356.2437 RESTRAINT = 0.0000 ESURF = 187.7125 minimization completed, ENE= -.10788908E+05 RMS= 0.173208E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0713E+04 1.7234E+01 1.1938E+02 N 4970 BOND = 1403.6013 ANGLE = 3695.4915 DIHED = 5424.7660 VDWAALS = -3954.2545 EEL = -34622.1075 EGB = -7992.0318 1-4 VDW = 1817.0255 1-4 EEL = 23327.0391 RESTRAINT = 0.0000 ESURF = 187.0316 minimization completed, ENE= -.10713439E+05 RMS= 0.172344E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0697E+04 1.7488E+01 1.1748E+02 N 5364 BOND = 1402.3296 ANGLE = 3761.5462 DIHED = 5495.2310 VDWAALS = -3865.3279 EEL = -34879.3611 EGB = -7922.7943 1-4 VDW = 1796.8050 1-4 EEL = 23325.6457 RESTRAINT = 0.0000 ESURF = 188.5146 minimization completed, ENE= -.10697411E+05 RMS= 0.174876E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0696E+04 1.7314E+01 1.2528E+02 C 7192 BOND = 1434.3278 ANGLE = 3706.3173 DIHED = 5407.8267 VDWAALS = -3891.9456 EEL = -34880.7708 EGB = -7853.1766 1-4 VDW = 1823.0226 1-4 EEL = 23371.0351 RESTRAINT = 0.0000 ESURF = 187.1960 minimization completed, ENE= -.10696168E+05 RMS= 0.173145E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0629E+04 1.7437E+01 1.0366E+02 CB 5628 BOND = 1449.6646 ANGLE = 3729.4468 DIHED = 5475.7923 VDWAALS = -3866.7709 EEL = -35003.6587 EGB = -7821.7945 1-4 VDW = 1822.5958 1-4 EEL = 23396.5544 RESTRAINT = 0.0000 ESURF = 189.5840 minimization completed, ENE= -.10628586E+05 RMS= 0.174368E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0814E+04 1.7279E+01 1.1827E+02 CG 129 BOND = 1411.4008 ANGLE = 3674.9550 DIHED = 5389.2761 VDWAALS = -3897.8625 EEL = -34706.1292 EGB = -7966.1716 1-4 VDW = 1810.0201 1-4 EEL = 23281.1427 RESTRAINT = 0.0000 ESURF = 189.6723 minimization completed, ENE= -.10813696E+05 RMS= 0.172787E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0694E+04 1.7523E+01 1.1853E+02 C 4248 BOND = 1468.2987 ANGLE = 3736.3719 DIHED = 5383.2468 VDWAALS = -3877.5926 EEL = -34681.8325 EGB = -8024.1536 1-4 VDW = 1803.0911 1-4 EEL = 23309.7452 RESTRAINT = 0.0000 ESURF = 188.8424 minimization completed, ENE= -.10693983E+05 RMS= 0.175230E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0732E+04 1.7265E+01 9.9280E+01 C 5456 BOND = 1421.0236 ANGLE = 3758.4200 DIHED = 5453.8981 VDWAALS = -3908.0274 EEL = -35037.3743 EGB = -7696.0520 1-4 VDW = 1789.7435 1-4 EEL = 23300.6010 RESTRAINT = 0.0000 ESURF = 186.2380 minimization completed, ENE= -.10731530E+05 RMS= 0.172649E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0792E+04 1.7184E+01 1.1115E+02 C 2806 BOND = 1411.6096 ANGLE = 3715.7197 DIHED = 5447.2850 VDWAALS = -3905.5332 EEL = -34881.9452 EGB = -7824.4668 1-4 VDW = 1807.7165 1-4 EEL = 23251.3286 RESTRAINT = 0.0000 ESURF = 186.6986 minimization completed, ENE= -.10791587E+05 RMS= 0.171845E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0765E+04 1.7353E+01 1.1852E+02 CG 1287 BOND = 1390.0747 ANGLE = 3708.4303 DIHED = 5462.3891 VDWAALS = -3925.0717 EEL = -35010.8066 EGB = -7708.6514 1-4 VDW = 1802.3648 1-4 EEL = 23331.1170 RESTRAINT = 0.0000 ESURF = 185.2495 minimization completed, ENE= -.10764904E+05 RMS= 0.173533E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0760E+04 1.7442E+01 1.2680E+02 CD 2779 BOND = 1420.4788 ANGLE = 3742.4913 DIHED = 5416.0818 VDWAALS = -3942.1353 EEL = -34866.6103 EGB = -7880.5703 1-4 VDW = 1782.7025 1-4 EEL = 23380.1983 RESTRAINT = 0.0000 ESURF = 187.8011 minimization completed, ENE= -.10759562E+05 RMS= 0.174419E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0722E+04 1.7220E+01 1.0636E+02 N 220 BOND = 1439.4453 ANGLE = 3821.8978 DIHED = 5394.9475 VDWAALS = -3919.1862 EEL = -34859.4588 EGB = -7870.1954 1-4 VDW = 1774.3918 1-4 EEL = 23309.5159 RESTRAINT = 0.0000 ESURF = 187.1130 minimization completed, ENE= -.10721529E+05 RMS= 0.172204E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0724E+04 1.7302E+01 1.2007E+02 C 5044 BOND = 1441.0048 ANGLE = 3764.4418 DIHED = 5416.4265 VDWAALS = -3904.4492 EEL = -34828.1699 EGB = -7812.8421 1-4 VDW = 1780.9132 1-4 EEL = 23231.7657 RESTRAINT = 0.0000 ESURF = 186.5398 minimization completed, ENE= -.10724369E+05 RMS= 0.173024E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0715E+04 1.7543E+01 1.2110E+02 CG 4170 BOND = 1436.9125 ANGLE = 3764.1236 DIHED = 5398.1557 VDWAALS = -3904.0210 EEL = -34846.6089 EGB = -7919.1931 1-4 VDW = 1810.5954 1-4 EEL = 23357.8868 RESTRAINT = 0.0000 ESURF = 187.1652 minimization completed, ENE= -.10714984E+05 RMS= 0.175427E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0714E+04 1.7150E+01 1.3961E+02 CG 617 BOND = 1403.7192 ANGLE = 3786.3367 DIHED = 5437.1778 VDWAALS = -3963.7396 EEL = -34836.7486 EGB = -7860.1901 1-4 VDW = 1822.9178 1-4 EEL = 23312.5637 RESTRAINT = 0.0000 ESURF = 183.7442 minimization completed, ENE= -.10714219E+05 RMS= 0.171501E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0757E+04 1.7240E+01 1.0323E+02 C 1349 BOND = 1409.6170 ANGLE = 3715.3170 DIHED = 5390.3384 VDWAALS = -3926.6300 EEL = -34884.0032 EGB = -7810.2674 1-4 VDW = 1802.1543 1-4 EEL = 23364.1809 RESTRAINT = 0.0000 ESURF = 182.1824 minimization completed, ENE= -.10757110E+05 RMS= 0.172403E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0740E+04 1.7360E+01 1.3034E+02 C 2086 BOND = 1452.3933 ANGLE = 3752.5636 DIHED = 5393.0082 VDWAALS = -3984.2447 EEL = -34894.2186 EGB = -7741.7443 1-4 VDW = 1788.3420 1-4 EEL = 23311.9311 RESTRAINT = 0.0000 ESURF = 181.8878 minimization completed, ENE= -.10740082E+05 RMS= 0.173604E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0796E+04 1.7347E+01 1.2303E+02 CG 6991 BOND = 1445.4111 ANGLE = 3654.1845 DIHED = 5398.8847 VDWAALS = -3920.0857 EEL = -34936.7689 EGB = -7789.1819 1-4 VDW = 1832.2922 1-4 EEL = 23336.4039 RESTRAINT = 0.0000 ESURF = 182.4451 minimization completed, ENE= -.10796415E+05 RMS= 0.173469E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0619E+04 1.7272E+01 1.1035E+02 C 4859 BOND = 1426.1197 ANGLE = 3816.1996 DIHED = 5441.0328 VDWAALS = -3897.1718 EEL = -34896.7834 EGB = -7793.6444 1-4 VDW = 1809.6945 1-4 EEL = 23289.3299 RESTRAINT = 0.0000 ESURF = 185.9606 minimization completed, ENE= -.10619263E+05 RMS= 0.172720E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0664E+04 1.7615E+01 1.0941E+02 CG 2050 BOND = 1447.2947 ANGLE = 3759.8200 DIHED = 5382.4753 VDWAALS = -3944.0627 EEL = -34752.0548 EGB = -7958.3140 1-4 VDW = 1826.6493 1-4 EEL = 23390.6139 RESTRAINT = 0.0000 ESURF = 184.0175 minimization completed, ENE= -.10663561E+05 RMS= 0.176147E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0684E+04 1.7386E+01 1.1156E+02 C 7788 BOND = 1427.8911 ANGLE = 3779.0907 DIHED = 5445.2507 VDWAALS = -3926.4010 EEL = -34709.9520 EGB = -7973.1476 1-4 VDW = 1789.4128 1-4 EEL = 23300.4028 RESTRAINT = 0.0000 ESURF = 183.3503 minimization completed, ENE= -.10684102E+05 RMS= 0.173856E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0704E+04 1.7198E+01 1.0599E+02 C 4525 BOND = 1359.3703 ANGLE = 3723.2538 DIHED = 5465.7279 VDWAALS = -3865.6738 EEL = -34791.1997 EGB = -7957.4683 1-4 VDW = 1824.6180 1-4 EEL = 23350.6640 RESTRAINT = 0.0000 ESURF = 186.3140 minimization completed, ENE= -.10704394E+05 RMS= 0.171975E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0711E+04 1.7336E+01 1.2912E+02 C 1103 BOND = 1441.7792 ANGLE = 3756.0651 DIHED = 5422.7906 VDWAALS = -3869.7113 EEL = -34691.9644 EGB = -8030.2533 1-4 VDW = 1779.5733 1-4 EEL = 23292.0619 RESTRAINT = 0.0000 ESURF = 188.8768 minimization completed, ENE= -.10710782E+05 RMS= 0.173358E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0804E+04 1.7068E+01 1.0034E+02 C 4407 BOND = 1400.4521 ANGLE = 3719.3437 DIHED = 5434.2166 VDWAALS = -3893.7893 EEL = -34804.1805 EGB = -7972.1668 1-4 VDW = 1809.2803 1-4 EEL = 23317.2858 RESTRAINT = 0.0000 ESURF = 185.8786 minimization completed, ENE= -.10803679E+05 RMS= 0.170684E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0729E+04 1.7102E+01 1.3070E+02 C 21 BOND = 1418.3359 ANGLE = 3776.4563 DIHED = 5419.8574 VDWAALS = -3952.2241 EEL = -34660.2231 EGB = -8013.4777 1-4 VDW = 1791.6959 1-4 EEL = 23305.7861 RESTRAINT = 0.0000 ESURF = 184.9561 minimization completed, ENE= -.10728837E+05 RMS= 0.171017E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0752E+04 1.7195E+01 9.9774E+01 C 4018 BOND = 1453.8332 ANGLE = 3694.2113 DIHED = 5415.0396 VDWAALS = -3877.1623 EEL = -34883.8327 EGB = -7912.5945 1-4 VDW = 1804.8793 1-4 EEL = 23369.7415 RESTRAINT = 0.0000 ESURF = 184.0390 minimization completed, ENE= -.10751846E+05 RMS= 0.171951E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0701E+04 1.7234E+01 1.2118E+02 C 4364 BOND = 1418.6537 ANGLE = 3668.3622 DIHED = 5421.6190 VDWAALS = -3947.9395 EEL = -34656.7552 EGB = -7962.4723 1-4 VDW = 1816.5863 1-4 EEL = 23357.8056 RESTRAINT = 0.0000 ESURF = 183.6255 minimization completed, ENE= -.10700515E+05 RMS= 0.172340E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0688E+04 1.7409E+01 1.3786E+02 C 490 BOND = 1400.9560 ANGLE = 3740.9600 DIHED = 5456.4838 VDWAALS = -3911.9314 EEL = -34822.6130 EGB = -7922.3953 1-4 VDW = 1812.1675 1-4 EEL = 23374.4028 RESTRAINT = 0.0000 ESURF = 184.1162 minimization completed, ENE= -.10687853E+05 RMS= 0.174092E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0680E+04 1.7234E+01 9.7211E+01 CG 7383 BOND = 1419.5237 ANGLE = 3780.2560 DIHED = 5402.1088 VDWAALS = -3914.0143 EEL = -34628.7000 EGB = -8004.4378 1-4 VDW = 1802.5013 1-4 EEL = 23276.8385 RESTRAINT = 0.0000 ESURF = 185.6681 minimization completed, ENE= -.10680256E+05 RMS= 0.172341E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0739E+04 1.7071E+01 1.1462E+02 C 1949 BOND = 1430.2119 ANGLE = 3698.1651 DIHED = 5400.5440 VDWAALS = -3847.7146 EEL = -34753.6794 EGB = -7937.2986 1-4 VDW = 1777.4230 1-4 EEL = 23307.8839 RESTRAINT = 0.0000 ESURF = 185.8931 minimization completed, ENE= -.10738572E+05 RMS= 0.170712E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0737E+04 1.7533E+01 1.1481E+02 CG 1674 BOND = 1437.6224 ANGLE = 3650.0077 DIHED = 5443.4047 VDWAALS = -3876.2576 EEL = -34811.7814 EGB = -8006.5628 1-4 VDW = 1804.7964 1-4 EEL = 23438.1341 RESTRAINT = 0.0000 ESURF = 183.2863 minimization completed, ENE= -.10737350E+05 RMS= 0.175328E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0705E+04 1.7468E+01 1.2866E+02 N 5174 BOND = 1468.3940 ANGLE = 3734.5257 DIHED = 5397.4852 VDWAALS = -3937.5789 EEL = -34789.3704 EGB = -7906.3882 1-4 VDW = 1828.4826 1-4 EEL = 23314.7743 RESTRAINT = 0.0000 ESURF = 184.4370 minimization completed, ENE= -.10705239E+05 RMS= 0.174684E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 682.39 ( 7.59% of Gen B) | Calc gb diag 5321.31 (59.22% of Gen B) | Calc gb off-diag 2981.74 (33.18% of Gen B) | Gen Born time 8985.45 (100.0% of Nonbo) | Nonbond force 8985.45 (99.88% of Force) | Bond/Angle/Dihedral 10.90 ( 0.12% of Force) | Force time 8996.36 (100.0% of Runmd) | Runmd Time 8996.36 (99.08% of Total) | Other 83.90 ( 0.92% of Total) | Total time 9080.28 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 00:30:16.539 on 10/20/2010 | Setup done at 00:30:17.455 on 10/20/2010 | Run done at 03:01:36.822 on 10/20/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/20/2010 at 00:30:16 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _lig.out.3 |INPCRD: 1XCK_chainA_MGATP_noWAT.inpcrd | PARM: 1XCK_chainA_MGATP_noWAT.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _lig.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 = 09/24/09 Time = 02:43:23 NATOM = 7879 NTYPES = 18 NBONH = 3991 MBONA = 3917 NTHETH = 9115 MTHETA = 5297 NPHIH = 17023 MPHIA = 12427 NHPARM = 0 NPARM = 0 NNB = 43422 NRES = 526 NBONA = 3917 NTHETA = 5297 NPHIA = 12427 NUMBND = 52 NUMANG = 108 NPTRA = 66 NATYP = 36 NPHB = 0 IFBOX = 0 NMXRS = 43 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 567848 | Hollerith 24165 | Integer 1061772 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 8678 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 -1.0739E+04 1.7363E+01 1.1732E+02 N 6014 BOND = 1392.4934 ANGLE = 3731.1828 DIHED = 5406.4865 VDWAALS = -3920.7329 EEL = -35169.3516 EGB = -7555.3749 1-4 VDW = 1812.8801 1-4 EEL = 23380.6958 RESTRAINT = 0.0000 ESURF = 182.5022 minimization completed, ENE= -.10739219E+05 RMS= 0.173634E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0659E+04 1.7307E+01 1.1992E+02 C 4949 BOND = 1370.3000 ANGLE = 3790.0512 DIHED = 5430.5381 VDWAALS = -3884.1075 EEL = -34961.4920 EGB = -7642.7125 1-4 VDW = 1813.4349 1-4 EEL = 23241.6990 RESTRAINT = 0.0000 ESURF = 182.7903 minimization completed, ENE= -.10659499E+05 RMS= 0.173069E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0664E+04 1.7498E+01 1.1563E+02 C 1768 BOND = 1441.9430 ANGLE = 3787.1431 DIHED = 5420.4753 VDWAALS = -3899.1475 EEL = -35143.2738 EGB = -7541.3491 1-4 VDW = 1806.2187 1-4 EEL = 23283.1922 RESTRAINT = 0.0000 ESURF = 180.8436 minimization completed, ENE= -.10663955E+05 RMS= 0.174985E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0651E+04 1.7529E+01 1.1186E+02 CG 2429 BOND = 1415.5652 ANGLE = 3770.7376 DIHED = 5447.9271 VDWAALS = -3883.3997 EEL = -35240.7125 EGB = -7492.3835 1-4 VDW = 1823.4462 1-4 EEL = 23326.3974 RESTRAINT = 0.0000 ESURF = 181.4493 minimization completed, ENE= -.10650973E+05 RMS= 0.175290E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0649E+04 1.7561E+01 1.1081E+02 C 134 BOND = 1472.7687 ANGLE = 3811.8332 DIHED = 5461.0299 VDWAALS = -3921.2168 EEL = -35067.7516 EGB = -7594.2817 1-4 VDW = 1806.6444 1-4 EEL = 23200.3978 RESTRAINT = 0.0000 ESURF = 181.8081 minimization completed, ENE= -.10648768E+05 RMS= 0.175608E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0768E+04 1.7316E+01 1.2192E+02 CA 319 BOND = 1424.7750 ANGLE = 3711.8111 DIHED = 5379.3985 VDWAALS = -3869.8866 EEL = -35114.5095 EGB = -7628.8478 1-4 VDW = 1811.7997 1-4 EEL = 23333.8819 RESTRAINT = 0.0000 ESURF = 183.8185 minimization completed, ENE= -.10767759E+05 RMS= 0.173161E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0660E+04 1.7335E+01 1.4759E+02 C 2330 BOND = 1408.6783 ANGLE = 3731.4678 DIHED = 5481.2025 VDWAALS = -3894.9399 EEL = -35090.7051 EGB = -7666.4429 1-4 VDW = 1811.1956 1-4 EEL = 23373.9081 RESTRAINT = 0.0000 ESURF = 185.3824 minimization completed, ENE= -.10660253E+05 RMS= 0.173346E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0679E+04 1.7489E+01 9.7331E+01 CG 3517 BOND = 1458.6984 ANGLE = 3718.8375 DIHED = 5410.2789 VDWAALS = -3884.6100 EEL = -35054.1682 EGB = -7635.3917 1-4 VDW = 1804.7683 1-4 EEL = 23318.9094 RESTRAINT = 0.0000 ESURF = 183.7025 minimization completed, ENE= -.10678975E+05 RMS= 0.174894E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0618E+04 1.7365E+01 1.0493E+02 CG1 5676 BOND = 1456.7775 ANGLE = 3790.2890 DIHED = 5412.0092 VDWAALS = -3921.4892 EEL = -34904.0611 EGB = -7769.5522 1-4 VDW = 1802.7731 1-4 EEL = 23331.9963 RESTRAINT = 0.0000 ESURF = 183.0865 minimization completed, ENE= -.10618171E+05 RMS= 0.173646E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0699E+04 1.7397E+01 1.1656E+02 C 1648 BOND = 1415.9775 ANGLE = 3824.0943 DIHED = 5388.5050 VDWAALS = -3910.0085 EEL = -35045.5931 EGB = -7649.6357 1-4 VDW = 1815.9033 1-4 EEL = 23279.4013 RESTRAINT = 0.0000 ESURF = 182.4725 minimization completed, ENE= -.10698883E+05 RMS= 0.173967E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0641E+04 1.7601E+01 1.2909E+02 C 6878 BOND = 1440.9448 ANGLE = 3866.6895 DIHED = 5390.1175 VDWAALS = -3962.5751 EEL = -34995.0845 EGB = -7663.0826 1-4 VDW = 1809.0024 1-4 EEL = 23288.9777 RESTRAINT = 0.0000 ESURF = 183.7297 minimization completed, ENE= -.10641280E+05 RMS= 0.176014E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0656E+04 1.7403E+01 1.0940E+02 CA 4529 BOND = 1431.8799 ANGLE = 3833.1856 DIHED = 5442.7397 VDWAALS = -3939.6124 EEL = -35237.0085 EGB = -7508.9410 1-4 VDW = 1802.9592 1-4 EEL = 23336.7693 RESTRAINT = 0.0000 ESURF = 182.5275 minimization completed, ENE= -.10655501E+05 RMS= 0.174025E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0744E+04 1.7319E+01 1.1654E+02 N 400 BOND = 1424.9177 ANGLE = 3739.6541 DIHED = 5490.2397 VDWAALS = -3914.6365 EEL = -35223.4754 EGB = -7515.7079 1-4 VDW = 1764.8260 1-4 EEL = 23306.9189 RESTRAINT = 0.0000 ESURF = 183.1200 minimization completed, ENE= -.10744143E+05 RMS= 0.173192E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0710E+04 1.7478E+01 1.2306E+02 C 1893 BOND = 1427.0518 ANGLE = 3774.4369 DIHED = 5408.3972 VDWAALS = -3925.3601 EEL = -35086.5876 EGB = -7641.6679 1-4 VDW = 1821.2121 1-4 EEL = 23329.8980 RESTRAINT = 0.0000 ESURF = 183.0112 minimization completed, ENE= -.10709608E+05 RMS= 0.174784E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0746E+04 1.7128E+01 1.0403E+02 C 1215 BOND = 1380.9835 ANGLE = 3750.4712 DIHED = 5454.7542 VDWAALS = -3945.9382 EEL = -34995.6802 EGB = -7722.3632 1-4 VDW = 1795.3209 1-4 EEL = 23353.9648 RESTRAINT = 0.0000 ESURF = 182.8641 minimization completed, ENE= -.10745623E+05 RMS= 0.171281E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0730E+04 1.7329E+01 1.1179E+02 C 4551 BOND = 1465.1613 ANGLE = 3676.7683 DIHED = 5418.9140 VDWAALS = -3887.8164 EEL = -34949.2933 EGB = -7737.9460 1-4 VDW = 1826.7298 1-4 EEL = 23274.6525 RESTRAINT = 0.0000 ESURF = 182.4737 minimization completed, ENE= -.10730356E+05 RMS= 0.173288E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0735E+04 1.7373E+01 1.2078E+02 CG 2686 BOND = 1378.0958 ANGLE = 3743.5904 DIHED = 5404.8415 VDWAALS = -3901.6977 EEL = -35114.2550 EGB = -7666.1991 1-4 VDW = 1823.9187 1-4 EEL = 23413.8176 RESTRAINT = 0.0000 ESURF = 183.1564 minimization completed, ENE= -.10734731E+05 RMS= 0.173726E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0726E+04 1.7314E+01 1.1521E+02 CA 4003 BOND = 1434.0622 ANGLE = 3742.9569 DIHED = 5417.9560 VDWAALS = -3902.9130 EEL = -35159.3346 EGB = -7573.9806 1-4 VDW = 1818.0266 1-4 EEL = 23313.6345 RESTRAINT = 0.0000 ESURF = 183.8008 minimization completed, ENE= -.10725791E+05 RMS= 0.173140E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0814E+04 1.7030E+01 1.0659E+02 C 7800 BOND = 1344.7152 ANGLE = 3756.7222 DIHED = 5424.9785 VDWAALS = -3910.9501 EEL = -35200.6563 EGB = -7533.3308 1-4 VDW = 1778.5172 1-4 EEL = 23343.4701 RESTRAINT = 0.0000 ESURF = 182.6969 minimization completed, ENE= -.10813837E+05 RMS= 0.170303E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0706E+04 1.7430E+01 1.2712E+02 CG 4342 BOND = 1474.0780 ANGLE = 3753.5122 DIHED = 5394.7620 VDWAALS = -3910.2414 EEL = -35066.4376 EGB = -7613.3944 1-4 VDW = 1782.9682 1-4 EEL = 23297.5629 RESTRAINT = 0.0000 ESURF = 181.2989 minimization completed, ENE= -.10705891E+05 RMS= 0.174301E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0790E+04 1.7409E+01 1.1549E+02 C 7312 BOND = 1490.1721 ANGLE = 3662.1608 DIHED = 5404.8506 VDWAALS = -3890.6491 EEL = -35101.0574 EGB = -7631.4354 1-4 VDW = 1790.8372 1-4 EEL = 23303.1719 RESTRAINT = 0.0000 ESURF = 181.9001 minimization completed, ENE= -.10790049E+05 RMS= 0.174087E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0742E+04 1.7145E+01 1.0995E+02 N 2472 BOND = 1398.4663 ANGLE = 3666.6383 DIHED = 5443.7168 VDWAALS = -3906.3687 EEL = -35120.9357 EGB = -7546.9017 1-4 VDW = 1811.2802 1-4 EEL = 23330.2831 RESTRAINT = 0.0000 ESURF = 181.6349 minimization completed, ENE= -.10742186E+05 RMS= 0.171449E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0684E+04 1.7563E+01 1.3903E+02 C 2806 BOND = 1469.9478 ANGLE = 3727.5458 DIHED = 5441.8673 VDWAALS = -3876.0138 EEL = -35217.5252 EGB = -7638.6377 1-4 VDW = 1805.6664 1-4 EEL = 23420.3838 RESTRAINT = 0.0000 ESURF = 182.9243 minimization completed, ENE= -.10683841E+05 RMS= 0.175632E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0881E+04 1.7155E+01 1.1373E+02 C 4108 BOND = 1392.8992 ANGLE = 3699.3308 DIHED = 5393.0459 VDWAALS = -3899.0198 EEL = -35130.0909 EGB = -7625.2621 1-4 VDW = 1773.8171 1-4 EEL = 23330.6421 RESTRAINT = 0.0000 ESURF = 183.7597 minimization completed, ENE= -.10880878E+05 RMS= 0.171550E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0811E+04 1.7334E+01 1.4279E+02 CD 7542 BOND = 1395.1469 ANGLE = 3708.5322 DIHED = 5404.6434 VDWAALS = -3916.3647 EEL = -35277.9018 EGB = -7508.4102 1-4 VDW = 1834.1393 1-4 EEL = 23367.4828 RESTRAINT = 0.0000 ESURF = 182.0709 minimization completed, ENE= -.10810661E+05 RMS= 0.173336E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0690E+04 1.7555E+01 1.2299E+02 C 3653 BOND = 1450.5806 ANGLE = 3749.0950 DIHED = 5415.9187 VDWAALS = -3926.2406 EEL = -35312.5362 EGB = -7451.2850 1-4 VDW = 1828.0283 1-4 EEL = 23376.4645 RESTRAINT = 0.0000 ESURF = 179.5051 minimization completed, ENE= -.10690470E+05 RMS= 0.175554E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0696E+04 1.7369E+01 1.1497E+02 C 2613 BOND = 1428.4402 ANGLE = 3736.1006 DIHED = 5428.6462 VDWAALS = -3934.3943 EEL = -35196.2666 EGB = -7573.8713 1-4 VDW = 1832.8890 1-4 EEL = 23399.7467 RESTRAINT = 0.0000 ESURF = 182.2247 minimization completed, ENE= -.10696485E+05 RMS= 0.173690E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0751E+04 1.7313E+01 1.0061E+02 C 4345 BOND = 1409.0164 ANGLE = 3743.7555 DIHED = 5393.2774 VDWAALS = -3889.6598 EEL = -35329.0375 EGB = -7485.3898 1-4 VDW = 1821.3741 1-4 EEL = 23404.1457 RESTRAINT = 0.0000 ESURF = 181.6737 minimization completed, ENE= -.10750844E+05 RMS= 0.173126E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0706E+04 1.7548E+01 1.6420E+02 C 1006 BOND = 1455.7451 ANGLE = 3759.6485 DIHED = 5422.5469 VDWAALS = -3888.4356 EEL = -35399.3964 EGB = -7443.0892 1-4 VDW = 1825.7335 1-4 EEL = 23379.8462 RESTRAINT = 0.0000 ESURF = 181.3945 minimization completed, ENE= -.10706007E+05 RMS= 0.175478E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0787E+04 1.7191E+01 1.0946E+02 C 7758 BOND = 1395.4420 ANGLE = 3780.9494 DIHED = 5441.4153 VDWAALS = -3933.6477 EEL = -35178.8421 EGB = -7551.5782 1-4 VDW = 1798.5029 1-4 EEL = 23279.3238 RESTRAINT = 0.0000 ESURF = 181.8072 minimization completed, ENE= -.10786627E+05 RMS= 0.171915E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0777E+04 1.7448E+01 1.1995E+02 C 573 BOND = 1451.4224 ANGLE = 3737.2728 DIHED = 5408.8848 VDWAALS = -3882.4478 EEL = -35163.8541 EGB = -7558.5293 1-4 VDW = 1797.6509 1-4 EEL = 23250.5394 RESTRAINT = 0.0000 ESURF = 181.5715 minimization completed, ENE= -.10777490E+05 RMS= 0.174479E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0772E+04 1.7311E+01 1.1873E+02 CG 5392 BOND = 1451.4901 ANGLE = 3705.4497 DIHED = 5427.1251 VDWAALS = -3943.7877 EEL = -35162.6968 EGB = -7550.0501 1-4 VDW = 1776.5700 1-4 EEL = 23342.5371 RESTRAINT = 0.0000 ESURF = 181.1023 minimization completed, ENE= -.10772260E+05 RMS= 0.173108E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0691E+04 1.7412E+01 1.1223E+02 C 146 BOND = 1429.4425 ANGLE = 3819.4138 DIHED = 5425.1718 VDWAALS = -3896.9610 EEL = -35129.3202 EGB = -7630.5707 1-4 VDW = 1802.6470 1-4 EEL = 23309.1907 RESTRAINT = 0.0000 ESURF = 180.4168 minimization completed, ENE= -.10690569E+05 RMS= 0.174124E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0787E+04 1.7108E+01 1.1202E+02 C 4428 BOND = 1382.5760 ANGLE = 3700.3634 DIHED = 5440.5742 VDWAALS = -3889.1501 EEL = -35167.2761 EGB = -7582.7143 1-4 VDW = 1813.9105 1-4 EEL = 23331.1546 RESTRAINT = 0.0000 ESURF = 183.0723 minimization completed, ENE= -.10787490E+05 RMS= 0.171077E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0745E+04 1.7262E+01 1.1650E+02 CZ 6294 BOND = 1451.8305 ANGLE = 3701.9650 DIHED = 5428.8666 VDWAALS = -3943.8029 EEL = -34993.6273 EGB = -7607.3856 1-4 VDW = 1800.6594 1-4 EEL = 23234.5383 RESTRAINT = 0.0000 ESURF = 181.7654 minimization completed, ENE= -.10745191E+05 RMS= 0.172621E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0700E+04 1.7285E+01 1.1528E+02 C 3937 BOND = 1395.4245 ANGLE = 3769.3609 DIHED = 5413.1202 VDWAALS = -3885.1185 EEL = -35142.5839 EGB = -7585.0905 1-4 VDW = 1800.2806 1-4 EEL = 23351.2236 RESTRAINT = 0.0000 ESURF = 183.2497 minimization completed, ENE= -.10700133E+05 RMS= 0.172846E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0728E+04 1.7228E+01 1.1610E+02 N 4074 BOND = 1416.1402 ANGLE = 3761.1919 DIHED = 5421.7302 VDWAALS = -3916.6073 EEL = -35154.2807 EGB = -7649.9581 1-4 VDW = 1796.6778 1-4 EEL = 23415.2249 RESTRAINT = 0.0000 ESURF = 182.3071 minimization completed, ENE= -.10727574E+05 RMS= 0.172280E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0713E+04 1.7420E+01 1.0315E+02 C 2053 BOND = 1454.9352 ANGLE = 3722.8151 DIHED = 5398.2929 VDWAALS = -3894.8973 EEL = -35073.5457 EGB = -7701.7189 1-4 VDW = 1822.8589 1-4 EEL = 23374.9985 RESTRAINT = 0.0000 ESURF = 183.3278 minimization completed, ENE= -.10712933E+05 RMS= 0.174195E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0756E+04 1.7085E+01 1.1102E+02 C 6715 BOND = 1384.0235 ANGLE = 3742.4867 DIHED = 5373.9820 VDWAALS = -3950.0731 EEL = -35005.8791 EGB = -7693.6040 1-4 VDW = 1817.1247 1-4 EEL = 23391.7408 RESTRAINT = 0.0000 ESURF = 183.8525 minimization completed, ENE= -.10756346E+05 RMS= 0.170849E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0800E+04 1.7203E+01 1.0710E+02 C 2641 BOND = 1368.8363 ANGLE = 3747.6128 DIHED = 5397.2433 VDWAALS = -3939.3384 EEL = -35266.9805 EGB = -7535.4715 1-4 VDW = 1838.1775 1-4 EEL = 23408.0242 RESTRAINT = 0.0000 ESURF = 182.2662 minimization completed, ENE= -.10799630E+05 RMS= 0.172030E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0679E+04 1.7392E+01 1.1330E+02 CZ 2986 BOND = 1395.2619 ANGLE = 3771.4630 DIHED = 5397.6002 VDWAALS = -3914.8420 EEL = -35251.6844 EGB = -7455.7695 1-4 VDW = 1835.0465 1-4 EEL = 23362.6275 RESTRAINT = 0.0000 ESURF = 180.8829 minimization completed, ENE= -.10679414E+05 RMS= 0.173923E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0720E+04 1.7265E+01 1.1157E+02 C 7055 BOND = 1400.5808 ANGLE = 3759.1848 DIHED = 5431.9152 VDWAALS = -3913.7262 EEL = -35047.4172 EGB = -7725.4593 1-4 VDW = 1821.9257 1-4 EEL = 23367.9205 RESTRAINT = 0.0000 ESURF = 185.3337 minimization completed, ENE= -.10719742E+05 RMS= 0.172650E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0672E+04 1.7381E+01 1.1285E+02 CG 782 BOND = 1409.9066 ANGLE = 3813.5169 DIHED = 5456.5297 VDWAALS = -3900.2293 EEL = -35026.5253 EGB = -7680.7145 1-4 VDW = 1795.6533 1-4 EEL = 23275.8789 RESTRAINT = 0.0000 ESURF = 184.2273 minimization completed, ENE= -.10671756E+05 RMS= 0.173810E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0682E+04 1.7384E+01 1.1599E+02 CG 7383 BOND = 1389.0054 ANGLE = 3725.1543 DIHED = 5451.1110 VDWAALS = -3895.1966 EEL = -35118.4466 EGB = -7622.5619 1-4 VDW = 1835.6323 1-4 EEL = 23369.4165 RESTRAINT = 0.0000 ESURF = 184.1237 minimization completed, ENE= -.10681762E+05 RMS= 0.173844E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0780E+04 1.7213E+01 1.2663E+02 CD 5297 BOND = 1421.8279 ANGLE = 3691.1958 DIHED = 5428.8752 VDWAALS = -3879.2044 EEL = -35138.0524 EGB = -7629.7237 1-4 VDW = 1825.4537 1-4 EEL = 23313.6605 RESTRAINT = 0.0000 ESURF = 186.2651 minimization completed, ENE= -.10779702E+05 RMS= 0.172128E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0722E+04 1.7282E+01 1.1842E+02 C 5638 BOND = 1430.2892 ANGLE = 3767.8929 DIHED = 5446.4891 VDWAALS = -3875.6478 EEL = -35197.3664 EGB = -7587.1028 1-4 VDW = 1818.9603 1-4 EEL = 23287.9846 RESTRAINT = 0.0000 ESURF = 186.4919 minimization completed, ENE= -.10722009E+05 RMS= 0.172818E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0643E+04 1.7597E+01 1.2532E+02 CA 4899 BOND = 1427.4419 ANGLE = 3859.5828 DIHED = 5440.6709 VDWAALS = -3925.8125 EEL = -35122.7860 EGB = -7620.0813 1-4 VDW = 1801.0845 1-4 EEL = 23311.8821 RESTRAINT = 0.0000 ESURF = 185.0169 minimization completed, ENE= -.10643001E+05 RMS= 0.175966E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0767E+04 1.7065E+01 1.2353E+02 CD1 7105 BOND = 1353.1821 ANGLE = 3777.3273 DIHED = 5437.3959 VDWAALS = -3931.5749 EEL = -34999.0040 EGB = -7730.4816 1-4 VDW = 1793.4407 1-4 EEL = 23349.0589 RESTRAINT = 0.0000 ESURF = 184.0246 minimization completed, ENE= -.10766631E+05 RMS= 0.170651E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0783E+04 1.7127E+01 1.0934E+02 N 7402 BOND = 1390.1590 ANGLE = 3775.4049 DIHED = 5401.6234 VDWAALS = -3936.2494 EEL = -35068.3096 EGB = -7660.3082 1-4 VDW = 1799.1291 1-4 EEL = 23332.9010 RESTRAINT = 0.0000 ESURF = 183.1327 minimization completed, ENE= -.10782517E+05 RMS= 0.171268E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0744E+04 1.7188E+01 1.1165E+02 NE 6435 BOND = 1386.4570 ANGLE = 3764.6892 DIHED = 5433.1121 VDWAALS = -3880.2781 EEL = -35057.0268 EGB = -7620.8646 1-4 VDW = 1778.3503 1-4 EEL = 23269.1736 RESTRAINT = 0.0000 ESURF = 182.1607 minimization completed, ENE= -.10744227E+05 RMS= 0.171880E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 669.22 ( 7.47% of Gen B) | Calc gb diag 5329.67 (59.53% of Gen B) | Calc gb off-diag 2953.95 (32.99% of Gen B) | Gen Born time 8952.84 (100.0% of Nonbo) | Nonbond force 8952.84 (99.89% of Force) | Bond/Angle/Dihedral 9.56 ( 0.11% of Force) | Force time 8962.41 (100.0% of Runmd) | Runmd Time 8962.41 (98.52% of Total) | Other 134.60 ( 1.48% of Total) | Total time 9097.03 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 00:30:16.458 on 10/20/2010 | Setup done at 00:30:17.501 on 10/20/2010 | Run done at 03:01:53.492 on 10/20/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/20/2010 at 00:30:16 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _lig.out.2 |INPCRD: 1XCK_chainA_MGATP_noWAT.inpcrd | PARM: 1XCK_chainA_MGATP_noWAT.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _lig.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 = 09/24/09 Time = 02:43:23 NATOM = 7879 NTYPES = 18 NBONH = 3991 MBONA = 3917 NTHETH = 9115 MTHETA = 5297 NPHIH = 17023 MPHIA = 12427 NHPARM = 0 NPARM = 0 NNB = 43422 NRES = 526 NBONA = 3917 NTHETA = 5297 NPHIA = 12427 NUMBND = 52 NUMANG = 108 NPTRA = 66 NATYP = 36 NPHB = 0 IFBOX = 0 NMXRS = 43 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 567848 | Hollerith 24165 | Integer 1061772 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 8678 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 -1.0795E+04 1.7005E+01 1.2304E+02 C 1620 BOND = 1359.0655 ANGLE = 3707.0433 DIHED = 5404.8224 VDWAALS = -3976.6401 EEL = -34909.0055 EGB = -7752.1507 1-4 VDW = 1822.6727 1-4 EEL = 23369.3989 RESTRAINT = 0.0000 ESURF = 179.4617 minimization completed, ENE= -.10795332E+05 RMS= 0.170052E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0695E+04 1.7279E+01 1.1604E+02 CG 995 BOND = 1419.1033 ANGLE = 3815.3925 DIHED = 5439.9007 VDWAALS = -3892.3113 EEL = -35094.7225 EGB = -7618.4686 1-4 VDW = 1790.7522 1-4 EEL = 23265.0193 RESTRAINT = 0.0000 ESURF = 180.5095 minimization completed, ENE= -.10694825E+05 RMS= 0.172786E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0809E+04 1.6957E+01 1.3029E+02 C 986 BOND = 1344.6647 ANGLE = 3654.9489 DIHED = 5428.6687 VDWAALS = -3929.7554 EEL = -34932.8885 EGB = -7811.6707 1-4 VDW = 1831.3662 1-4 EEL = 23424.6222 RESTRAINT = 0.0000 ESURF = 180.7714 minimization completed, ENE= -.10809273E+05 RMS= 0.169570E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0681E+04 1.7569E+01 1.1362E+02 C 642 BOND = 1432.6366 ANGLE = 3797.4258 DIHED = 5437.7566 VDWAALS = -3872.9706 EEL = -34894.7576 EGB = -7827.9097 1-4 VDW = 1799.3894 1-4 EEL = 23265.8804 RESTRAINT = 0.0000 ESURF = 181.5477 minimization completed, ENE= -.10681001E+05 RMS= 0.175690E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0721E+04 1.7369E+01 1.0585E+02 CA 849 BOND = 1426.1268 ANGLE = 3771.4627 DIHED = 5426.5603 VDWAALS = -3925.7582 EEL = -35098.0864 EGB = -7646.0304 1-4 VDW = 1809.7169 1-4 EEL = 23332.5746 RESTRAINT = 0.0000 ESURF = 182.2949 minimization completed, ENE= -.10721139E+05 RMS= 0.173690E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0721E+04 1.7376E+01 1.3706E+02 C 7701 BOND = 1366.6531 ANGLE = 3790.0015 DIHED = 5433.6148 VDWAALS = -3897.9012 EEL = -35007.2137 EGB = -7778.1320 1-4 VDW = 1837.6050 1-4 EEL = 23352.9286 RESTRAINT = 0.0000 ESURF = 181.6273 minimization completed, ENE= -.10720816E+05 RMS= 0.173764E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0810E+04 1.7355E+01 1.0653E+02 C 3427 BOND = 1398.3689 ANGLE = 3660.5531 DIHED = 5400.0725 VDWAALS = -3880.0606 EEL = -34793.1251 EGB = -7854.0811 1-4 VDW = 1799.6166 1-4 EEL = 23275.2511 RESTRAINT = 0.0000 ESURF = 183.8283 minimization completed, ENE= -.10809576E+05 RMS= 0.173550E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0700E+04 1.7589E+01 1.3138E+02 C 7243 BOND = 1442.2939 ANGLE = 3720.8053 DIHED = 5456.8003 VDWAALS = -3917.9924 EEL = -34955.6324 EGB = -7741.5530 1-4 VDW = 1802.1322 1-4 EEL = 23310.1519 RESTRAINT = 0.0000 ESURF = 183.1442 minimization completed, ENE= -.10699850E+05 RMS= 0.175887E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0724E+04 1.7350E+01 1.1938E+02 CG 3379 BOND = 1471.0460 ANGLE = 3705.9966 DIHED = 5454.2605 VDWAALS = -3928.5056 EEL = -34737.8332 EGB = -7861.6697 1-4 VDW = 1765.3536 1-4 EEL = 23224.5790 RESTRAINT = 0.0000 ESURF = 182.4407 minimization completed, ENE= -.10724332E+05 RMS= 0.173503E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0681E+04 1.7374E+01 1.1631E+02 C 7625 BOND = 1454.5938 ANGLE = 3741.6600 DIHED = 5440.4728 VDWAALS = -3917.7400 EEL = -34841.4572 EGB = -7784.1025 1-4 VDW = 1803.3993 1-4 EEL = 23240.0603 RESTRAINT = 0.0000 ESURF = 181.7832 minimization completed, ENE= -.10681330E+05 RMS= 0.173737E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0764E+04 1.7277E+01 1.0070E+02 C 7833 BOND = 1390.4162 ANGLE = 3760.9446 DIHED = 5417.6686 VDWAALS = -3917.3800 EEL = -35097.5381 EGB = -7667.0238 1-4 VDW = 1851.1128 1-4 EEL = 23317.5140 RESTRAINT = 0.0000 ESURF = 180.4786 minimization completed, ENE= -.10763807E+05 RMS= 0.172766E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0770E+04 1.7178E+01 1.0994E+02 C 156 BOND = 1374.9163 ANGLE = 3690.4821 DIHED = 5432.4743 VDWAALS = -3933.8833 EEL = -35064.0992 EGB = -7637.8271 1-4 VDW = 1782.3056 1-4 EEL = 23404.0142 RESTRAINT = 0.0000 ESURF = 181.3572 minimization completed, ENE= -.10770260E+05 RMS= 0.171777E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0732E+04 1.7227E+01 1.2880E+02 C 1297 BOND = 1412.1419 ANGLE = 3728.2815 DIHED = 5405.3794 VDWAALS = -3914.5234 EEL = -35005.5085 EGB = -7681.3288 1-4 VDW = 1829.5811 1-4 EEL = 23313.2626 RESTRAINT = 0.0000 ESURF = 180.8197 minimization completed, ENE= -.10731895E+05 RMS= 0.172274E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0845E+04 1.7236E+01 1.0860E+02 CD 5859 BOND = 1423.9295 ANGLE = 3695.8735 DIHED = 5406.6022 VDWAALS = -3938.6414 EEL = -34954.8392 EGB = -7759.9862 1-4 VDW = 1770.7436 1-4 EEL = 23330.0620 RESTRAINT = 0.0000 ESURF = 181.5738 minimization completed, ENE= -.10844682E+05 RMS= 0.172355E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0663E+04 1.7668E+01 1.3108E+02 CA 6501 BOND = 1456.0325 ANGLE = 3799.1151 DIHED = 5409.4984 VDWAALS = -3906.8182 EEL = -35141.9217 EGB = -7653.8936 1-4 VDW = 1830.3814 1-4 EEL = 23362.7517 RESTRAINT = 0.0000 ESURF = 182.1197 minimization completed, ENE= -.10662735E+05 RMS= 0.176677E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0729E+04 1.7180E+01 1.1004E+02 C 1261 BOND = 1370.8391 ANGLE = 3754.2640 DIHED = 5436.4849 VDWAALS = -3944.0005 EEL = -34744.4222 EGB = -7886.9417 1-4 VDW = 1832.3825 1-4 EEL = 23270.4774 RESTRAINT = 0.0000 ESURF = 182.4008 minimization completed, ENE= -.10728515E+05 RMS= 0.171803E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0763E+04 1.7494E+01 1.2300E+02 C 7026 BOND = 1429.5079 ANGLE = 3692.5363 DIHED = 5411.0026 VDWAALS = -3892.0644 EEL = -34926.3107 EGB = -7791.3197 1-4 VDW = 1791.6299 1-4 EEL = 23337.9138 RESTRAINT = 0.0000 ESURF = 184.2766 minimization completed, ENE= -.10762828E+05 RMS= 0.174944E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0735E+04 1.7362E+01 1.2139E+02 C 1502 BOND = 1424.9385 ANGLE = 3707.1223 DIHED = 5424.5108 VDWAALS = -3944.2799 EEL = -34845.3890 EGB = -7795.7144 1-4 VDW = 1821.7876 1-4 EEL = 23289.2248 RESTRAINT = 0.0000 ESURF = 183.0221 minimization completed, ENE= -.10734777E+05 RMS= 0.173618E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0778E+04 1.7396E+01 1.2378E+02 CG 617 BOND = 1461.0334 ANGLE = 3731.8432 DIHED = 5406.0585 VDWAALS = -3911.0508 EEL = -34955.0306 EGB = -7734.3757 1-4 VDW = 1765.9210 1-4 EEL = 23273.8096 RESTRAINT = 0.0000 ESURF = 184.2769 minimization completed, ENE= -.10777515E+05 RMS= 0.173965E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0688E+04 1.7406E+01 1.2397E+02 N 7802 BOND = 1477.1549 ANGLE = 3722.8174 DIHED = 5426.6804 VDWAALS = -3924.9157 EEL = -34732.1825 EGB = -7940.7414 1-4 VDW = 1812.6696 1-4 EEL = 23286.4734 RESTRAINT = 0.0000 ESURF = 183.7905 minimization completed, ENE= -.10688253E+05 RMS= 0.174059E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0760E+04 1.7209E+01 1.0854E+02 C 7250 BOND = 1391.8370 ANGLE = 3672.9870 DIHED = 5459.5285 VDWAALS = -3873.0201 EEL = -35227.1335 EGB = -7626.4528 1-4 VDW = 1847.3518 1-4 EEL = 23411.9435 RESTRAINT = 0.0000 ESURF = 182.9017 minimization completed, ENE= -.10760057E+05 RMS= 0.172085E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0603E+04 1.7319E+01 1.2884E+02 CB 6824 BOND = 1421.8568 ANGLE = 3834.2895 DIHED = 5417.4284 VDWAALS = -3920.8832 EEL = -34954.1210 EGB = -7734.9454 1-4 VDW = 1799.2246 1-4 EEL = 23354.7907 RESTRAINT = 0.0000 ESURF = 178.8704 minimization completed, ENE= -.10603489E+05 RMS= 0.173195E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0705E+04 1.7286E+01 1.0690E+02 C 4859 BOND = 1363.6152 ANGLE = 3749.7885 DIHED = 5433.8994 VDWAALS = -3903.5525 EEL = -34858.4362 EGB = -7764.2395 1-4 VDW = 1803.3220 1-4 EEL = 23289.0277 RESTRAINT = 0.0000 ESURF = 181.1261 minimization completed, ENE= -.10705449E+05 RMS= 0.172863E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0754E+04 1.7284E+01 1.3315E+02 N 2516 BOND = 1368.1329 ANGLE = 3768.4828 DIHED = 5420.6376 VDWAALS = -3920.3270 EEL = -35023.9135 EGB = -7674.1482 1-4 VDW = 1810.0387 1-4 EEL = 23315.8312 RESTRAINT = 0.0000 ESURF = 181.3767 minimization completed, ENE= -.10753889E+05 RMS= 0.172837E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0761E+04 1.7639E+01 1.0231E+02 C 2041 BOND = 1456.7976 ANGLE = 3778.7945 DIHED = 5413.0268 VDWAALS = -3955.1883 EEL = -34853.7485 EGB = -7836.6696 1-4 VDW = 1780.3646 1-4 EEL = 23273.9264 RESTRAINT = 0.0000 ESURF = 181.7098 minimization completed, ENE= -.10760987E+05 RMS= 0.176390E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0662E+04 1.7363E+01 1.1752E+02 C 3197 BOND = 1467.2887 ANGLE = 3803.9284 DIHED = 5428.1421 VDWAALS = -3924.9906 EEL = -34806.5915 EGB = -7825.7708 1-4 VDW = 1781.2414 1-4 EEL = 23231.9457 RESTRAINT = 0.0000 ESURF = 182.4254 minimization completed, ENE= -.10662381E+05 RMS= 0.173632E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0704E+04 1.7382E+01 1.2733E+02 N 6511 BOND = 1425.7571 ANGLE = 3822.1546 DIHED = 5415.7324 VDWAALS = -3842.0794 EEL = -34923.4011 EGB = -7769.8917 1-4 VDW = 1767.4159 1-4 EEL = 23214.4665 RESTRAINT = 0.0000 ESURF = 185.9485 minimization completed, ENE= -.10703897E+05 RMS= 0.173822E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0720E+04 1.7522E+01 1.2395E+02 C 2086 BOND = 1464.4000 ANGLE = 3689.7600 DIHED = 5453.3560 VDWAALS = -3874.5165 EEL = -34865.0301 EGB = -7803.2323 1-4 VDW = 1794.4076 1-4 EEL = 23236.6100 RESTRAINT = 0.0000 ESURF = 184.2317 minimization completed, ENE= -.10720014E+05 RMS= 0.175215E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0697E+04 1.7575E+01 1.2405E+02 C 5059 BOND = 1465.2799 ANGLE = 3750.4042 DIHED = 5413.8688 VDWAALS = -3878.3459 EEL = -34889.1557 EGB = -7756.2500 1-4 VDW = 1774.8594 1-4 EEL = 23238.9913 RESTRAINT = 0.0000 ESURF = 183.8040 minimization completed, ENE= -.10696544E+05 RMS= 0.175747E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0680E+04 1.7208E+01 1.2862E+02 C 4840 BOND = 1352.0143 ANGLE = 3778.8697 DIHED = 5422.4392 VDWAALS = -3874.6336 EEL = -34997.2613 EGB = -7775.7373 1-4 VDW = 1826.3840 1-4 EEL = 23404.8658 RESTRAINT = 0.0000 ESURF = 183.1344 minimization completed, ENE= -.10679925E+05 RMS= 0.172075E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0807E+04 1.7243E+01 1.1174E+02 C 6182 BOND = 1403.2302 ANGLE = 3711.2300 DIHED = 5395.8768 VDWAALS = -3849.8333 EEL = -35022.6351 EGB = -7777.3785 1-4 VDW = 1825.2531 1-4 EEL = 23325.3662 RESTRAINT = 0.0000 ESURF = 182.3564 minimization completed, ENE= -.10806534E+05 RMS= 0.172433E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0764E+04 1.7449E+01 1.0033E+02 CZ 173 BOND = 1420.1684 ANGLE = 3727.4752 DIHED = 5388.3722 VDWAALS = -3850.9549 EEL = -35065.2322 EGB = -7670.7099 1-4 VDW = 1810.3350 1-4 EEL = 23292.4459 RESTRAINT = 0.0000 ESURF = 183.9726 minimization completed, ENE= -.10764128E+05 RMS= 0.174492E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0767E+04 1.7252E+01 1.1562E+02 C 1006 BOND = 1402.5455 ANGLE = 3710.5519 DIHED = 5431.6594 VDWAALS = -3901.8337 EEL = -35042.2402 EGB = -7732.6262 1-4 VDW = 1818.7525 1-4 EEL = 23361.9534 RESTRAINT = 0.0000 ESURF = 183.9419 minimization completed, ENE= -.10767296E+05 RMS= 0.172515E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0734E+04 1.7673E+01 1.1568E+02 C 5339 BOND = 1484.1379 ANGLE = 3756.8907 DIHED = 5419.3269 VDWAALS = -3961.6151 EEL = -35105.8189 EGB = -7624.1386 1-4 VDW = 1788.4576 1-4 EEL = 23325.7095 RESTRAINT = 0.0000 ESURF = 183.3706 minimization completed, ENE= -.10733679E+05 RMS= 0.176728E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0779E+04 1.7253E+01 1.1682E+02 C 986 BOND = 1358.7561 ANGLE = 3795.9332 DIHED = 5446.3767 VDWAALS = -3900.3993 EEL = -35081.2419 EGB = -7667.6477 1-4 VDW = 1808.2769 1-4 EEL = 23277.2429 RESTRAINT = 0.0000 ESURF = 183.9967 minimization completed, ENE= -.10778706E+05 RMS= 0.172531E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0857E+04 1.7201E+01 1.1586E+02 N 1636 BOND = 1352.0705 ANGLE = 3667.0619 DIHED = 5455.8605 VDWAALS = -3894.8852 EEL = -35176.3333 EGB = -7626.3113 1-4 VDW = 1820.4668 1-4 EEL = 23362.7076 RESTRAINT = 0.0000 ESURF = 182.4823 minimization completed, ENE= -.10856880E+05 RMS= 0.172005E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0712E+04 1.7333E+01 1.1555E+02 C 4364 BOND = 1391.5178 ANGLE = 3755.7906 DIHED = 5400.4568 VDWAALS = -3894.8400 EEL = -35041.3090 EGB = -7652.1468 1-4 VDW = 1817.7353 1-4 EEL = 23328.8279 RESTRAINT = 0.0000 ESURF = 182.0588 minimization completed, ENE= -.10711908E+05 RMS= 0.173332E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0686E+04 1.7277E+01 1.1554E+02 C 2256 BOND = 1376.3099 ANGLE = 3765.8079 DIHED = 5408.1128 VDWAALS = -3932.0341 EEL = -35060.0335 EGB = -7636.1010 1-4 VDW = 1837.4115 1-4 EEL = 23371.8901 RESTRAINT = 0.0000 ESURF = 182.6964 minimization completed, ENE= -.10685940E+05 RMS= 0.172765E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0695E+04 1.7529E+01 1.0891E+02 C 2271 BOND = 1376.8433 ANGLE = 3826.3964 DIHED = 5393.6126 VDWAALS = -3932.9912 EEL = -35171.1178 EGB = -7558.1555 1-4 VDW = 1848.6408 1-4 EEL = 23340.0076 RESTRAINT = 0.0000 ESURF = 181.6288 minimization completed, ENE= -.10695135E+05 RMS= 0.175292E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0787E+04 1.7300E+01 1.3165E+02 C 680 BOND = 1460.4882 ANGLE = 3665.2712 DIHED = 5425.2817 VDWAALS = -3901.0710 EEL = -35042.1511 EGB = -7725.6721 1-4 VDW = 1811.1459 1-4 EEL = 23336.0231 RESTRAINT = 0.0000 ESURF = 183.8818 minimization completed, ENE= -.10786802E+05 RMS= 0.172999E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0797E+04 1.7281E+01 1.0743E+02 C 6620 BOND = 1412.4651 ANGLE = 3658.5155 DIHED = 5408.1690 VDWAALS = -3920.5918 EEL = -34902.6286 EGB = -7748.4470 1-4 VDW = 1817.1967 1-4 EEL = 23294.6864 RESTRAINT = 0.0000 ESURF = 183.4593 minimization completed, ENE= -.10797175E+05 RMS= 0.172812E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0720E+04 1.6959E+01 1.2624E+02 C 4374 BOND = 1392.9083 ANGLE = 3766.0430 DIHED = 5456.7217 VDWAALS = -3905.9942 EEL = -35049.8696 EGB = -7618.9809 1-4 VDW = 1799.8371 1-4 EEL = 23256.1055 RESTRAINT = 0.0000 ESURF = 183.5824 minimization completed, ENE= -.10719647E+05 RMS= 0.169591E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0635E+04 1.7626E+01 1.2690E+02 C 1893 BOND = 1429.5538 ANGLE = 3796.1078 DIHED = 5370.5313 VDWAALS = -3881.1765 EEL = -35078.4898 EGB = -7596.8468 1-4 VDW = 1811.6486 1-4 EEL = 23331.0336 RESTRAINT = 0.0000 ESURF = 183.0717 minimization completed, ENE= -.10634566E+05 RMS= 0.176263E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0764E+04 1.7422E+01 1.0488E+02 C 5862 BOND = 1412.7213 ANGLE = 3769.6517 DIHED = 5412.8654 VDWAALS = -3956.1031 EEL = -35158.4534 EGB = -7510.6370 1-4 VDW = 1809.0333 1-4 EEL = 23275.0735 RESTRAINT = 0.0000 ESURF = 182.2754 minimization completed, ENE= -.10763573E+05 RMS= 0.174219E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0709E+04 1.7460E+01 1.1637E+02 C 4808 BOND = 1441.4822 ANGLE = 3774.3912 DIHED = 5377.1020 VDWAALS = -3895.0831 EEL = -34930.3582 EGB = -7699.0417 1-4 VDW = 1783.3482 1-4 EEL = 23255.7344 RESTRAINT = 0.0000 ESURF = 183.0874 minimization completed, ENE= -.10709337E+05 RMS= 0.174604E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0775E+04 1.7256E+01 1.3641E+02 C 2219 BOND = 1398.5427 ANGLE = 3786.4672 DIHED = 5376.8530 VDWAALS = -3894.8033 EEL = -35192.7131 EGB = -7530.2058 1-4 VDW = 1803.4290 1-4 EEL = 23294.0217 RESTRAINT = 0.0000 ESURF = 183.8045 minimization completed, ENE= -.10774604E+05 RMS= 0.172564E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0862E+04 1.7137E+01 1.1939E+02 C 6150 BOND = 1409.1014 ANGLE = 3734.9900 DIHED = 5390.4124 VDWAALS = -3904.2569 EEL = -35033.1890 EGB = -7659.6288 1-4 VDW = 1774.0393 1-4 EEL = 23241.8950 RESTRAINT = 0.0000 ESURF = 184.6273 minimization completed, ENE= -.10862009E+05 RMS= 0.171367E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0728E+04 1.7295E+01 1.3245E+02 C 6401 BOND = 1434.0054 ANGLE = 3709.4915 DIHED = 5419.8218 VDWAALS = -3866.7320 EEL = -35144.3120 EGB = -7614.7870 1-4 VDW = 1817.0721 1-4 EEL = 23333.0487 RESTRAINT = 0.0000 ESURF = 184.5894 minimization completed, ENE= -.10727802E+05 RMS= 0.172954E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0752E+04 1.7290E+01 1.1992E+02 CD 7204 BOND = 1437.7436 ANGLE = 3769.5839 DIHED = 5376.6376 VDWAALS = -3878.1629 EEL = -35170.5586 EGB = -7543.4010 1-4 VDW = 1817.7436 1-4 EEL = 23253.7505 RESTRAINT = 0.0000 ESURF = 185.0695 minimization completed, ENE= -.10751594E+05 RMS= 0.172897E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0721E+04 1.7361E+01 1.0132E+02 CG 782 BOND = 1395.1678 ANGLE = 3764.0297 DIHED = 5442.2523 VDWAALS = -3911.2053 EEL = -35324.5280 EGB = -7318.7200 1-4 VDW = 1810.0510 1-4 EEL = 23239.4791 RESTRAINT = 0.0000 ESURF = 181.9844 minimization completed, ENE= -.10721489E+05 RMS= 0.173608E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 689.62 ( 7.66% of Gen B) | Calc gb diag 5329.27 (59.21% of Gen B) | Calc gb off-diag 2981.72 (33.13% of Gen B) | Gen Born time 9000.61 (100.0% of Nonbo) | Nonbond force 9000.61 (100.0% of Force) | Bond/Angle/Dihedral 7.49 ( 0.08% of Force) | Force time 9008.11 (100.0% of Runmd) | Runmd Time 9008.11 (99.05% of Total) | Other 86.79 ( 0.95% of Total) | Total time 9094.92 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 00:30:16.451 on 10/20/2010 | Setup done at 00:30:17.421 on 10/20/2010 | Run done at 03:01:51.376 on 10/20/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/20/2010 at 00:30:16 [-O]verwriting output File Assignments: | MDIN: gb.in | MDOUT: _lig.out.1 |INPCRD: 1XCK_chainA_MGATP_noWAT.inpcrd | PARM: 1XCK_chainA_MGATP_noWAT.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _lig.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 = 09/24/09 Time = 02:43:23 NATOM = 7879 NTYPES = 18 NBONH = 3991 MBONA = 3917 NTHETH = 9115 MTHETA = 5297 NPHIH = 17023 MPHIA = 12427 NHPARM = 0 NPARM = 0 NNB = 43422 NRES = 526 NBONA = 3917 NTHETA = 5297 NPHIA = 12427 NUMBND = 52 NUMANG = 108 NPTRA = 66 NATYP = 36 NPHB = 0 IFBOX = 0 NMXRS = 43 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 567848 | Hollerith 24165 | Integer 1061772 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 8678 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 -1.0717E+04 1.7501E+01 1.0749E+02 C 2767 BOND = 1442.2738 ANGLE = 3746.1996 DIHED = 5388.5552 VDWAALS = -3929.7175 EEL = -34866.1604 EGB = -7708.7408 1-4 VDW = 1780.6327 1-4 EEL = 23247.1740 RESTRAINT = 0.0000 ESURF = 182.3470 minimization completed, ENE= -.10717436E+05 RMS= 0.175014E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0752E+04 1.7362E+01 1.2141E+02 CA 5319 BOND = 1408.3523 ANGLE = 3684.1262 DIHED = 5440.5461 VDWAALS = -3930.2974 EEL = -34874.3713 EGB = -7815.9781 1-4 VDW = 1810.6436 1-4 EEL = 23340.7546 RESTRAINT = 0.0000 ESURF = 184.4569 minimization completed, ENE= -.10751767E+05 RMS= 0.173620E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0690E+04 1.7410E+01 1.1509E+02 C 2751 BOND = 1447.2949 ANGLE = 3748.6458 DIHED = 5418.4141 VDWAALS = -3926.4375 EEL = -34926.5123 EGB = -7790.5792 1-4 VDW = 1799.8429 1-4 EEL = 23356.2496 RESTRAINT = 0.0000 ESURF = 183.1277 minimization completed, ENE= -.10689954E+05 RMS= 0.174102E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0710E+04 1.7298E+01 1.1704E+02 C 2125 BOND = 1398.1350 ANGLE = 3710.5154 DIHED = 5422.0870 VDWAALS = -3909.3564 EEL = -35105.1101 EGB = -7618.0299 1-4 VDW = 1814.5380 1-4 EEL = 23395.3105 RESTRAINT = 0.0000 ESURF = 181.9786 minimization completed, ENE= -.10709932E+05 RMS= 0.172977E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0792E+04 1.7139E+01 1.2463E+02 CG 617 BOND = 1400.2812 ANGLE = 3714.7542 DIHED = 5430.8270 VDWAALS = -3931.6364 EEL = -34983.1480 EGB = -7703.8136 1-4 VDW = 1805.9348 1-4 EEL = 23292.6449 RESTRAINT = 0.0000 ESURF = 182.3431 minimization completed, ENE= -.10791813E+05 RMS= 0.171394E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0603E+04 1.7451E+01 1.1587E+02 C 4784 BOND = 1425.2717 ANGLE = 3713.7350 DIHED = 5456.4465 VDWAALS = -3940.7429 EEL = -34977.4698 EGB = -7668.6331 1-4 VDW = 1842.5322 1-4 EEL = 23364.7165 RESTRAINT = 0.0000 ESURF = 181.2225 minimization completed, ENE= -.10602921E+05 RMS= 0.174511E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0692E+04 1.7270E+01 1.2063E+02 C 2256 BOND = 1419.1061 ANGLE = 3718.3464 DIHED = 5408.3771 VDWAALS = -3887.4292 EEL = -34883.0136 EGB = -7784.0690 1-4 VDW = 1801.7904 1-4 EEL = 23332.3457 RESTRAINT = 0.0000 ESURF = 182.8788 minimization completed, ENE= -.10691667E+05 RMS= 0.172698E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0748E+04 1.7375E+01 1.2079E+02 CG 3932 BOND = 1443.6727 ANGLE = 3719.1168 DIHED = 5382.7591 VDWAALS = -3935.1155 EEL = -34978.3445 EGB = -7705.4034 1-4 VDW = 1825.4596 1-4 EEL = 23318.2235 RESTRAINT = 0.0000 ESURF = 181.2745 minimization completed, ENE= -.10748357E+05 RMS= 0.173748E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0688E+04 1.7186E+01 1.1115E+02 N 6145 BOND = 1412.8352 ANGLE = 3740.8116 DIHED = 5424.4677 VDWAALS = -3917.4153 EEL = -34835.9265 EGB = -7737.5178 1-4 VDW = 1798.5038 1-4 EEL = 23240.9549 RESTRAINT = 0.0000 ESURF = 185.1220 minimization completed, ENE= -.10688164E+05 RMS= 0.171858E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0837E+04 1.7158E+01 1.0781E+02 CZ 3211 BOND = 1420.4561 ANGLE = 3684.6315 DIHED = 5436.5555 VDWAALS = -3959.7735 EEL = -35037.3372 EGB = -7574.8448 1-4 VDW = 1772.3764 1-4 EEL = 23238.9587 RESTRAINT = 0.0000 ESURF = 181.6541 minimization completed, ENE= -.10837323E+05 RMS= 0.171583E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0762E+04 1.7111E+01 1.1796E+02 CZ 2965 BOND = 1390.9143 ANGLE = 3700.5717 DIHED = 5413.3561 VDWAALS = -3920.7560 EEL = -35154.5718 EGB = -7556.2563 1-4 VDW = 1830.9182 1-4 EEL = 23354.3028 RESTRAINT = 0.0000 ESURF = 179.9972 minimization completed, ENE= -.10761524E+05 RMS= 0.171110E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0720E+04 1.7399E+01 1.2149E+02 C 4602 BOND = 1396.0616 ANGLE = 3730.4969 DIHED = 5417.3094 VDWAALS = -3930.6779 EEL = -35140.1370 EGB = -7582.7898 1-4 VDW = 1833.5080 1-4 EEL = 23376.1827 RESTRAINT = 0.0000 ESURF = 179.8579 minimization completed, ENE= -.10720188E+05 RMS= 0.173989E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0660E+04 1.7335E+01 1.1213E+02 C 5956 BOND = 1463.6989 ANGLE = 3774.3011 DIHED = 5426.6868 VDWAALS = -3928.2540 EEL = -35141.9708 EGB = -7549.4616 1-4 VDW = 1802.7176 1-4 EEL = 23309.6965 RESTRAINT = 0.0000 ESURF = 182.2462 minimization completed, ENE= -.10660339E+05 RMS= 0.173346E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0791E+04 1.7264E+01 1.2481E+02 C 5266 BOND = 1418.3664 ANGLE = 3704.2640 DIHED = 5423.8180 VDWAALS = -3949.2911 EEL = -35089.2548 EGB = -7588.1293 1-4 VDW = 1797.6773 1-4 EEL = 23310.3164 RESTRAINT = 0.0000 ESURF = 181.4940 minimization completed, ENE= -.10790739E+05 RMS= 0.172638E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0724E+04 1.7470E+01 1.2775E+02 N 7802 BOND = 1458.5818 ANGLE = 3794.2786 DIHED = 5423.5392 VDWAALS = -3950.8782 EEL = -35240.0627 EGB = -7471.0815 1-4 VDW = 1786.2021 1-4 EEL = 23296.2202 RESTRAINT = 0.0000 ESURF = 178.8024 minimization completed, ENE= -.10724398E+05 RMS= 0.174703E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0634E+04 1.7520E+01 1.2505E+02 CD 3073 BOND = 1433.1559 ANGLE = 3763.1899 DIHED = 5429.0944 VDWAALS = -3908.7085 EEL = -35075.0067 EGB = -7615.0504 1-4 VDW = 1805.1281 1-4 EEL = 23354.1975 RESTRAINT = 0.0000 ESURF = 180.3022 minimization completed, ENE= -.10633698E+05 RMS= 0.175201E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0744E+04 1.7192E+01 1.2266E+02 CA 6624 BOND = 1412.7120 ANGLE = 3690.8468 DIHED = 5410.9765 VDWAALS = -3942.5635 EEL = -34925.9231 EGB = -7696.6645 1-4 VDW = 1819.4926 1-4 EEL = 23307.5499 RESTRAINT = 0.0000 ESURF = 179.4199 minimization completed, ENE= -.10744153E+05 RMS= 0.171922E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0773E+04 1.7231E+01 1.0719E+02 C 3427 BOND = 1397.1168 ANGLE = 3725.3360 DIHED = 5433.8851 VDWAALS = -3931.8754 EEL = -34967.3488 EGB = -7695.0806 1-4 VDW = 1812.2632 1-4 EEL = 23272.3681 RESTRAINT = 0.0000 ESURF = 180.4471 minimization completed, ENE= -.10772888E+05 RMS= 0.172310E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0752E+04 1.7322E+01 1.2713E+02 C 589 BOND = 1407.3461 ANGLE = 3696.1437 DIHED = 5409.2965 VDWAALS = -3959.5851 EEL = -34763.8428 EGB = -7838.8863 1-4 VDW = 1807.3242 1-4 EEL = 23307.9422 RESTRAINT = 0.0000 ESURF = 181.9581 minimization completed, ENE= -.10752304E+05 RMS= 0.173217E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0718E+04 1.7324E+01 1.2129E+02 C 4921 BOND = 1416.6758 ANGLE = 3765.4373 DIHED = 5439.9963 VDWAALS = -3918.4367 EEL = -35024.3473 EGB = -7685.0624 1-4 VDW = 1793.0692 1-4 EEL = 23314.5482 RESTRAINT = 0.0000 ESURF = 180.0537 minimization completed, ENE= -.10718066E+05 RMS= 0.173238E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0756E+04 1.7383E+01 1.2564E+02 C 2420 BOND = 1450.6665 ANGLE = 3700.4359 DIHED = 5376.6389 VDWAALS = -3947.7613 EEL = -35013.2219 EGB = -7668.2908 1-4 VDW = 1828.7916 1-4 EEL = 23336.8407 RESTRAINT = 0.0000 ESURF = 180.3234 minimization completed, ENE= -.10755577E+05 RMS= 0.173829E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0739E+04 1.7326E+01 1.1290E+02 C 2308 BOND = 1398.8193 ANGLE = 3774.9945 DIHED = 5415.4079 VDWAALS = -3952.6676 EEL = -35111.1099 EGB = -7546.8210 1-4 VDW = 1825.5590 1-4 EEL = 23276.3566 RESTRAINT = 0.0000 ESURF = 180.9540 minimization completed, ENE= -.10738507E+05 RMS= 0.173262E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0768E+04 1.7456E+01 1.0398E+02 CG 6477 BOND = 1444.9348 ANGLE = 3750.0824 DIHED = 5437.9611 VDWAALS = -3959.1699 EEL = -35088.7767 EGB = -7548.5147 1-4 VDW = 1809.5890 1-4 EEL = 23206.7492 RESTRAINT = 0.0000 ESURF = 179.0182 minimization completed, ENE= -.10768127E+05 RMS= 0.174557E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0676E+04 1.7566E+01 1.2962E+02 C 1560 BOND = 1455.5377 ANGLE = 3755.5346 DIHED = 5424.7518 VDWAALS = -3924.3646 EEL = -35100.9539 EGB = -7608.3486 1-4 VDW = 1815.7701 1-4 EEL = 23325.8583 RESTRAINT = 0.0000 ESURF = 179.9005 minimization completed, ENE= -.10676314E+05 RMS= 0.175658E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0751E+04 1.7215E+01 1.2315E+02 C 2613 BOND = 1393.4882 ANGLE = 3729.1210 DIHED = 5442.4882 VDWAALS = -3945.9471 EEL = -35110.3993 EGB = -7581.6680 1-4 VDW = 1804.7671 1-4 EEL = 23337.4693 RESTRAINT = 0.0000 ESURF = 179.2760 minimization completed, ENE= -.10751405E+05 RMS= 0.172147E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0703E+04 1.7528E+01 1.1662E+02 C 2556 BOND = 1432.6040 ANGLE = 3744.1839 DIHED = 5424.8994 VDWAALS = -3947.4769 EEL = -35061.6225 EGB = -7544.0063 1-4 VDW = 1777.3888 1-4 EEL = 23291.0827 RESTRAINT = 0.0000 ESURF = 179.5513 minimization completed, ENE= -.10703395E+05 RMS= 0.175276E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0697E+04 1.7568E+01 1.0252E+02 C 653 BOND = 1451.8024 ANGLE = 3740.0518 DIHED = 5431.8356 VDWAALS = -3974.3120 EEL = -34947.4435 EGB = -7737.2732 1-4 VDW = 1798.5307 1-4 EEL = 23358.6593 RESTRAINT = 0.0000 ESURF = 180.8547 minimization completed, ENE= -.10697294E+05 RMS= 0.175676E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0698E+04 1.7253E+01 1.0904E+02 C 5622 BOND = 1367.2263 ANGLE = 3814.6005 DIHED = 5455.5606 VDWAALS = -3934.9022 EEL = -34979.1305 EGB = -7676.1346 1-4 VDW = 1805.2782 1-4 EEL = 23269.5373 RESTRAINT = 0.0000 ESURF = 180.1027 minimization completed, ENE= -.10697862E+05 RMS= 0.172532E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0668E+04 1.7427E+01 1.0006E+02 CG1 7348 BOND = 1384.1614 ANGLE = 3731.4734 DIHED = 5460.2304 VDWAALS = -3964.5496 EEL = -35127.1386 EGB = -7604.1070 1-4 VDW = 1818.5606 1-4 EEL = 23452.2661 RESTRAINT = 0.0000 ESURF = 180.7083 minimization completed, ENE= -.10668395E+05 RMS= 0.174266E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0777E+04 1.7274E+01 1.1387E+02 C 5825 BOND = 1413.5510 ANGLE = 3699.4988 DIHED = 5440.5659 VDWAALS = -3921.4628 EEL = -34999.6605 EGB = -7654.7078 1-4 VDW = 1801.4832 1-4 EEL = 23263.3451 RESTRAINT = 0.0000 ESURF = 179.9344 minimization completed, ENE= -.10777453E+05 RMS= 0.172744E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0712E+04 1.7744E+01 1.1004E+02 CB 7306 BOND = 1500.6087 ANGLE = 3645.2657 DIHED = 5412.8010 VDWAALS = -3956.8926 EEL = -35224.3175 EGB = -7497.9543 1-4 VDW = 1817.2295 1-4 EEL = 23410.9139 RESTRAINT = 0.0000 ESURF = 180.5438 minimization completed, ENE= -.10711802E+05 RMS= 0.177442E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0699E+04 1.7384E+01 1.1328E+02 CZ 6437 BOND = 1426.7224 ANGLE = 3718.7357 DIHED = 5453.1033 VDWAALS = -3946.2780 EEL = -35050.6162 EGB = -7613.8312 1-4 VDW = 1825.3551 1-4 EEL = 23308.2198 RESTRAINT = 0.0000 ESURF = 179.3861 minimization completed, ENE= -.10699203E+05 RMS= 0.173838E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0831E+04 1.7308E+01 1.1881E+02 C 7055 BOND = 1413.0556 ANGLE = 3684.3664 DIHED = 5353.6049 VDWAALS = -3945.6243 EEL = -35127.0768 EGB = -7642.4504 1-4 VDW = 1814.7522 1-4 EEL = 23438.9505 RESTRAINT = 0.0000 ESURF = 179.7457 minimization completed, ENE= -.10830676E+05 RMS= 0.173076E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0757E+04 1.7294E+01 1.0670E+02 C 3653 BOND = 1364.7378 ANGLE = 3708.4546 DIHED = 5455.5893 VDWAALS = -3869.5992 EEL = -35239.3632 EGB = -7600.7056 1-4 VDW = 1802.4271 1-4 EEL = 23440.9741 RESTRAINT = 0.0000 ESURF = 180.7200 minimization completed, ENE= -.10756765E+05 RMS= 0.172943E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0691E+04 1.7636E+01 1.2425E+02 CA 7792 BOND = 1437.8139 ANGLE = 3776.5969 DIHED = 5403.8467 VDWAALS = -3908.7708 EEL = -35197.5622 EGB = -7536.1709 1-4 VDW = 1815.6560 1-4 EEL = 23337.6650 RESTRAINT = 0.0000 ESURF = 179.8943 minimization completed, ENE= -.10691031E+05 RMS= 0.176362E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0749E+04 1.7305E+01 1.0676E+02 C 6630 BOND = 1426.2532 ANGLE = 3679.4358 DIHED = 5435.9662 VDWAALS = -3941.3120 EEL = -35076.1491 EGB = -7591.0351 1-4 VDW = 1791.5317 1-4 EEL = 23344.4753 RESTRAINT = 0.0000 ESURF = 182.1637 minimization completed, ENE= -.10748670E+05 RMS= 0.173050E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0759E+04 1.7387E+01 1.0300E+02 C 3829 BOND = 1426.5587 ANGLE = 3670.0995 DIHED = 5418.2814 VDWAALS = -3892.4160 EEL = -35109.6513 EGB = -7632.3879 1-4 VDW = 1830.5353 1-4 EEL = 23348.7555 RESTRAINT = 0.0000 ESURF = 180.9832 minimization completed, ENE= -.10759242E+05 RMS= 0.173869E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0816E+04 1.7384E+01 1.2874E+02 C 6097 BOND = 1375.9486 ANGLE = 3795.5197 DIHED = 5418.7030 VDWAALS = -3934.4912 EEL = -35119.4986 EGB = -7626.0792 1-4 VDW = 1795.7127 1-4 EEL = 23297.5875 RESTRAINT = 0.0000 ESURF = 180.6244 minimization completed, ENE= -.10815973E+05 RMS= 0.173842E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0662E+04 1.7347E+01 1.0656E+02 CG 7797 BOND = 1395.9288 ANGLE = 3802.3639 DIHED = 5472.4731 VDWAALS = -3934.7207 EEL = -34936.7992 EGB = -7747.8680 1-4 VDW = 1787.5142 1-4 EEL = 23316.7293 RESTRAINT = 0.0000 ESURF = 182.0337 minimization completed, ENE= -.10662345E+05 RMS= 0.173472E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0793E+04 1.7444E+01 1.0880E+02 CD 1499 BOND = 1399.5675 ANGLE = 3775.7856 DIHED = 5406.7447 VDWAALS = -3951.7081 EEL = -34954.4228 EGB = -7746.1646 1-4 VDW = 1792.6668 1-4 EEL = 23303.5361 RESTRAINT = 0.0000 ESURF = 180.6615 minimization completed, ENE= -.10793333E+05 RMS= 0.174440E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0757E+04 1.7146E+01 1.0737E+02 CA 6393 BOND = 1373.7257 ANGLE = 3769.9072 DIHED = 5458.7960 VDWAALS = -3893.0595 EEL = -35056.3772 EGB = -7700.1327 1-4 VDW = 1793.5737 1-4 EEL = 23314.8287 RESTRAINT = 0.0000 ESURF = 181.7732 minimization completed, ENE= -.10756965E+05 RMS= 0.171456E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0765E+04 1.7462E+01 1.0750E+02 C 7312 BOND = 1458.7226 ANGLE = 3794.5620 DIHED = 5410.0048 VDWAALS = -3944.5047 EEL = -34994.7581 EGB = -7677.6269 1-4 VDW = 1787.0866 1-4 EEL = 23219.0422 RESTRAINT = 0.0000 ESURF = 182.5394 minimization completed, ENE= -.10764932E+05 RMS= 0.174619E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0713E+04 1.7495E+01 1.1247E+02 C 2514 BOND = 1436.0752 ANGLE = 3725.2784 DIHED = 5479.1521 VDWAALS = -3918.4952 EEL = -34770.8869 EGB = -7894.6521 1-4 VDW = 1781.2849 1-4 EEL = 23266.5959 RESTRAINT = 0.0000 ESURF = 182.2412 minimization completed, ENE= -.10713406E+05 RMS= 0.174954E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0626E+04 1.7352E+01 1.1295E+02 CD2 2905 BOND = 1453.5868 ANGLE = 3777.4980 DIHED = 5444.7467 VDWAALS = -3876.2642 EEL = -34731.4038 EGB = -7929.3610 1-4 VDW = 1788.1154 1-4 EEL = 23263.4947 RESTRAINT = 0.0000 ESURF = 183.5383 minimization completed, ENE= -.10626049E+05 RMS= 0.173517E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0753E+04 1.7208E+01 1.3127E+02 CA 2407 BOND = 1407.8346 ANGLE = 3628.0231 DIHED = 5427.3863 VDWAALS = -3933.9091 EEL = -34914.4564 EGB = -7749.3199 1-4 VDW = 1829.3498 1-4 EEL = 23370.2585 RESTRAINT = 0.0000 ESURF = 182.1221 minimization completed, ENE= -.10752711E+05 RMS= 0.172083E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0846E+04 1.7516E+01 1.1183E+02 C 751 BOND = 1443.3777 ANGLE = 3617.4135 DIHED = 5397.6973 VDWAALS = -3899.9699 EEL = -35056.9468 EGB = -7708.4329 1-4 VDW = 1814.9311 1-4 EEL = 23365.7514 RESTRAINT = 0.0000 ESURF = 180.1448 minimization completed, ENE= -.10846034E+05 RMS= 0.175163E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0830E+04 1.7118E+01 1.1852E+02 PB 7842 BOND = 1415.7526 ANGLE = 3647.6844 DIHED = 5406.3981 VDWAALS = -3916.4535 EEL = -35017.6120 EGB = -7635.6473 1-4 VDW = 1807.9814 1-4 EEL = 23280.5681 RESTRAINT = 0.0000 ESURF = 181.3410 minimization completed, ENE= -.10829987E+05 RMS= 0.171176E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0698E+04 1.7377E+01 1.2607E+02 CE2 3213 BOND = 1407.7915 ANGLE = 3719.6182 DIHED = 5408.8193 VDWAALS = -3920.9233 EEL = -34994.7613 EGB = -7703.1982 1-4 VDW = 1842.8364 1-4 EEL = 23361.5486 RESTRAINT = 0.0000 ESURF = 180.2907 minimization completed, ENE= -.10697978E+05 RMS= 0.173772E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0658E+04 1.7529E+01 1.1763E+02 C 4181 BOND = 1417.0767 ANGLE = 3807.1040 DIHED = 5416.9114 VDWAALS = -3932.9177 EEL = -35052.1200 EGB = -7642.0655 1-4 VDW = 1841.5790 1-4 EEL = 23304.5797 RESTRAINT = 0.0000 ESURF = 181.4777 minimization completed, ENE= -.10658375E+05 RMS= 0.175286E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0716E+04 1.7211E+01 1.5450E+02 C 7400 BOND = 1403.5082 ANGLE = 3680.9074 DIHED = 5447.8626 VDWAALS = -3894.1751 EEL = -34922.5918 EGB = -7800.5133 1-4 VDW = 1814.0284 1-4 EEL = 23374.9401 RESTRAINT = 0.0000 ESURF = 179.6405 minimization completed, ENE= -.10716393E+05 RMS= 0.172114E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 696.81 ( 7.73% of Gen B) | Calc gb diag 5365.86 (59.53% of Gen B) | Calc gb off-diag 2950.36 (32.73% of Gen B) | Gen Born time 9013.04 (100.0% of Nonbo) | Nonbond force 9013.04 (100.0% of Force) | Bond/Angle/Dihedral 6.16 ( 0.07% of Force) | Force time 9019.21 (100.0% of Runmd) | Runmd Time 9019.21 (99.06% of Total) | Other 85.51 ( 0.94% of Total) | Total time 9104.73 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 00:30:16.452 on 10/20/2010 | Setup done at 00:30:17.517 on 10/20/2010 | Run done at 03:02:01.184 on 10/20/2010 | wallclock() was called 1809 times