------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/19/2010 at 19:12:39 [-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 -1.0639E+04 1.7329E+01 1.1774E+02 C 6451 BOND = 1432.8473 ANGLE = 3858.4823 DIHED = 5412.2280 VDWAALS = -3932.3123 EEL = -35148.6467 EGB = -7466.0796 1-4 VDW = 1796.7538 1-4 EEL = 23227.5440 RESTRAINT = 0.0000 ESURF = 180.4806 minimization completed, ENE= -.10638703E+05 RMS= 0.173294E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0607E+04 1.7552E+01 1.3050E+02 C 4935 BOND = 1446.8171 ANGLE = 3830.1929 DIHED = 5460.0849 VDWAALS = -3947.0824 EEL = -35289.1017 EGB = -7402.0537 1-4 VDW = 1818.7280 1-4 EEL = 23294.5929 RESTRAINT = 0.0000 ESURF = 180.7245 minimization completed, ENE= -.10607098E+05 RMS= 0.175516E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0732E+04 1.7310E+01 1.0774E+02 CD 7219 BOND = 1396.8999 ANGLE = 3754.9703 DIHED = 5404.2694 VDWAALS = -3913.8756 EEL = -35183.7752 EGB = -7413.0201 1-4 VDW = 1826.1529 1-4 EEL = 23217.0910 RESTRAINT = 0.0000 ESURF = 179.0821 minimization completed, ENE= -.10732205E+05 RMS= 0.173102E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0774E+04 1.7218E+01 1.0358E+02 C 3672 BOND = 1376.0983 ANGLE = 3744.9027 DIHED = 5441.3575 VDWAALS = -3962.9889 EEL = -35307.1024 EGB = -7384.4214 1-4 VDW = 1810.6369 1-4 EEL = 23327.0020 RESTRAINT = 0.0000 ESURF = 180.3560 minimization completed, ENE= -.10774159E+05 RMS= 0.172183E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0823E+04 1.7124E+01 1.2249E+02 CZ 6437 BOND = 1365.0978 ANGLE = 3773.9130 DIHED = 5411.7520 VDWAALS = -3943.3685 EEL = -35206.4303 EGB = -7432.8936 1-4 VDW = 1828.2814 1-4 EEL = 23200.1034 RESTRAINT = 0.0000 ESURF = 180.3608 minimization completed, ENE= -.10823184E+05 RMS= 0.171240E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0829E+04 1.7191E+01 1.2477E+02 C 450 BOND = 1372.5624 ANGLE = 3761.4163 DIHED = 5383.0496 VDWAALS = -3924.9055 EEL = -35273.5111 EGB = -7416.6802 1-4 VDW = 1785.2186 1-4 EEL = 23302.4773 RESTRAINT = 0.0000 ESURF = 181.5142 minimization completed, ENE= -.10828858E+05 RMS= 0.171910E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0811E+04 1.7046E+01 1.2072E+02 CG 2852 BOND = 1346.0578 ANGLE = 3706.1771 DIHED = 5396.7177 VDWAALS = -3910.7056 EEL = -35397.4356 EGB = -7272.2689 1-4 VDW = 1834.6016 1-4 EEL = 23305.9647 RESTRAINT = 0.0000 ESURF = 179.7934 minimization completed, ENE= -.10811098E+05 RMS= 0.170458E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0691E+04 1.7550E+01 1.1755E+02 CA 6147 BOND = 1502.7613 ANGLE = 3699.1713 DIHED = 5433.9696 VDWAALS = -3913.0148 EEL = -35169.8580 EGB = -7438.0816 1-4 VDW = 1798.3437 1-4 EEL = 23214.1616 RESTRAINT = 0.0000 ESURF = 181.7933 minimization completed, ENE= -.10690754E+05 RMS= 0.175499E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0776E+04 1.7140E+01 1.1146E+02 C 4639 BOND = 1421.3928 ANGLE = 3787.3723 DIHED = 5402.9595 VDWAALS = -3980.4359 EEL = -35298.7047 EGB = -7361.1881 1-4 VDW = 1804.2111 1-4 EEL = 23266.8721 RESTRAINT = 0.0000 ESURF = 181.8164 minimization completed, ENE= -.10775704E+05 RMS= 0.171396E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0716E+04 1.7444E+01 1.2246E+02 C 4034 BOND = 1448.0043 ANGLE = 3685.7679 DIHED = 5435.9755 VDWAALS = -3893.6832 EEL = -35157.7392 EGB = -7592.1856 1-4 VDW = 1824.8677 1-4 EEL = 23349.8160 RESTRAINT = 0.0000 ESURF = 182.9636 minimization completed, ENE= -.10716213E+05 RMS= 0.174437E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0685E+04 1.7428E+01 1.0600E+02 CA 2436 BOND = 1422.3549 ANGLE = 3726.1950 DIHED = 5481.6827 VDWAALS = -3929.4830 EEL = -35335.7930 EGB = -7373.3282 1-4 VDW = 1810.2287 1-4 EEL = 23329.1855 RESTRAINT = 0.0000 ESURF = 183.9341 minimization completed, ENE= -.10685023E+05 RMS= 0.174282E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0651E+04 1.7246E+01 1.3804E+02 C 543 BOND = 1374.0665 ANGLE = 3803.5146 DIHED = 5437.4121 VDWAALS = -3911.4631 EEL = -35038.1963 EGB = -7648.4161 1-4 VDW = 1820.7810 1-4 EEL = 23327.8387 RESTRAINT = 0.0000 ESURF = 183.3572 minimization completed, ENE= -.10651105E+05 RMS= 0.172458E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0654E+04 1.7440E+01 1.2524E+02 C 6317 BOND = 1416.6238 ANGLE = 3793.6047 DIHED = 5445.2049 VDWAALS = -3962.1901 EEL = -34898.3431 EGB = -7682.1169 1-4 VDW = 1803.6293 1-4 EEL = 23249.0051 RESTRAINT = 0.0000 ESURF = 180.9566 minimization completed, ENE= -.10653626E+05 RMS= 0.174402E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0602E+04 1.7525E+01 1.1289E+02 CD2 7566 BOND = 1459.7173 ANGLE = 3865.5369 DIHED = 5389.0269 VDWAALS = -3888.7457 EEL = -35143.5074 EGB = -7555.3262 1-4 VDW = 1829.5480 1-4 EEL = 23259.7353 RESTRAINT = 0.0000 ESURF = 182.3410 minimization completed, ENE= -.10601674E+05 RMS= 0.175248E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0837E+04 1.7182E+01 1.5388E+02 C 6087 BOND = 1386.0188 ANGLE = 3695.7616 DIHED = 5437.0350 VDWAALS = -3933.3212 EEL = -35240.8692 EGB = -7517.9854 1-4 VDW = 1809.3210 1-4 EEL = 23345.2479 RESTRAINT = 0.0000 ESURF = 181.7460 minimization completed, ENE= -.10837046E+05 RMS= 0.171823E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0739E+04 1.7418E+01 1.1310E+02 C 1172 BOND = 1439.4227 ANGLE = 3757.6145 DIHED = 5365.5704 VDWAALS = -3892.9960 EEL = -35252.3399 EGB = -7402.6780 1-4 VDW = 1806.0793 1-4 EEL = 23259.2424 RESTRAINT = 0.0000 ESURF = 181.3348 minimization completed, ENE= -.10738750E+05 RMS= 0.174181E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0754E+04 1.7381E+01 1.1044E+02 C 4510 BOND = 1400.1399 ANGLE = 3810.9121 DIHED = 5398.0185 VDWAALS = -3917.1714 EEL = -35225.9008 EGB = -7479.1594 1-4 VDW = 1798.4603 1-4 EEL = 23278.5473 RESTRAINT = 0.0000 ESURF = 182.3410 minimization completed, ENE= -.10753813E+05 RMS= 0.173807E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0810E+04 1.7166E+01 1.0572E+02 C 3907 BOND = 1385.9161 ANGLE = 3780.8017 DIHED = 5377.6821 VDWAALS = -3952.7756 EEL = -35226.2191 EGB = -7445.0286 1-4 VDW = 1782.9770 1-4 EEL = 23304.2481 RESTRAINT = 0.0000 ESURF = 182.5265 minimization completed, ENE= -.10809872E+05 RMS= 0.171661E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0692E+04 1.7575E+01 1.1211E+02 C 2879 BOND = 1462.1576 ANGLE = 3729.5028 DIHED = 5437.3273 VDWAALS = -3898.9882 EEL = -35298.5297 EGB = -7418.9909 1-4 VDW = 1807.8759 1-4 EEL = 23306.5442 RESTRAINT = 0.0000 ESURF = 181.5734 minimization completed, ENE= -.10691528E+05 RMS= 0.175746E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0637E+04 1.7585E+01 1.1517E+02 C 4188 BOND = 1457.0291 ANGLE = 3781.7788 DIHED = 5426.8117 VDWAALS = -3928.4042 EEL = -35156.7325 EGB = -7526.0265 1-4 VDW = 1786.7764 1-4 EEL = 23341.3719 RESTRAINT = 0.0000 ESURF = 180.3007 minimization completed, ENE= -.10637095E+05 RMS= 0.175854E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0810E+04 1.7184E+01 1.0774E+02 N 2380 BOND = 1376.9705 ANGLE = 3746.3025 DIHED = 5369.9773 VDWAALS = -3892.6260 EEL = -35180.2097 EGB = -7473.1634 1-4 VDW = 1797.4909 1-4 EEL = 23262.5057 RESTRAINT = 0.0000 ESURF = 182.4957 minimization completed, ENE= -.10810257E+05 RMS= 0.171839E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0898E+04 1.7139E+01 1.1696E+02 C 3829 BOND = 1367.4003 ANGLE = 3706.6530 DIHED = 5341.2795 VDWAALS = -3934.8584 EEL = -35069.0169 EGB = -7532.3173 1-4 VDW = 1816.1145 1-4 EEL = 23225.1579 RESTRAINT = 0.0000 ESURF = 181.9510 minimization completed, ENE= -.10897637E+05 RMS= 0.171392E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0727E+04 1.7239E+01 1.1444E+02 CA 2847 BOND = 1373.4542 ANGLE = 3855.0181 DIHED = 5382.5042 VDWAALS = -3909.6181 EEL = -35179.6758 EGB = -7588.6865 1-4 VDW = 1829.9520 1-4 EEL = 23325.9220 RESTRAINT = 0.0000 ESURF = 183.7082 minimization completed, ENE= -.10727422E+05 RMS= 0.172388E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0724E+04 1.7381E+01 1.1033E+02 CG 2960 BOND = 1443.3215 ANGLE = 3802.4129 DIHED = 5386.0679 VDWAALS = -3921.6569 EEL = -35199.5002 EGB = -7508.1465 1-4 VDW = 1804.7850 1-4 EEL = 23286.6775 RESTRAINT = 0.0000 ESURF = 182.2576 minimization completed, ENE= -.10723781E+05 RMS= 0.173814E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0755E+04 1.7131E+01 1.1231E+02 C 1251 BOND = 1424.8037 ANGLE = 3700.2245 DIHED = 5379.4936 VDWAALS = -3895.1433 EEL = -35233.4193 EGB = -7462.5374 1-4 VDW = 1810.8446 1-4 EEL = 23339.0139 RESTRAINT = 0.0000 ESURF = 181.4826 minimization completed, ENE= -.10755237E+05 RMS= 0.171306E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0808E+04 1.7169E+01 1.3660E+02 C 4808 BOND = 1396.0727 ANGLE = 3728.8678 DIHED = 5408.2502 VDWAALS = -3903.0350 EEL = -35132.0468 EGB = -7603.3560 1-4 VDW = 1821.5303 1-4 EEL = 23295.6235 RESTRAINT = 0.0000 ESURF = 180.2371 minimization completed, ENE= -.10807856E+05 RMS= 0.171692E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0829E+04 1.7373E+01 1.1175E+02 C 6166 BOND = 1453.4315 ANGLE = 3631.7150 DIHED = 5404.5980 VDWAALS = -3939.6391 EEL = -35110.4465 EGB = -7588.2056 1-4 VDW = 1817.4849 1-4 EEL = 23321.8277 RESTRAINT = 0.0000 ESURF = 180.2266 minimization completed, ENE= -.10829007E+05 RMS= 0.173728E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0731E+04 1.7406E+01 1.1816E+02 C 3284 BOND = 1450.7876 ANGLE = 3765.2502 DIHED = 5383.9193 VDWAALS = -4014.1207 EEL = -35138.4079 EGB = -7509.3102 1-4 VDW = 1813.1261 1-4 EEL = 23336.1101 RESTRAINT = 0.0000 ESURF = 181.2207 minimization completed, ENE= -.10731425E+05 RMS= 0.174059E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0760E+04 1.7359E+01 1.2462E+02 NH1 3986 BOND = 1402.7057 ANGLE = 3712.3771 DIHED = 5412.2229 VDWAALS = -3968.5599 EEL = -35244.5965 EGB = -7434.8823 1-4 VDW = 1818.5725 1-4 EEL = 23361.9613 RESTRAINT = 0.0000 ESURF = 179.7417 minimization completed, ENE= -.10760458E+05 RMS= 0.173590E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0622E+04 1.7494E+01 1.0837E+02 N 1143 BOND = 1435.1738 ANGLE = 3836.1176 DIHED = 5427.7379 VDWAALS = -3900.7615 EEL = -35159.8041 EGB = -7477.6955 1-4 VDW = 1785.5565 1-4 EEL = 23248.2700 RESTRAINT = 0.0000 ESURF = 183.2076 minimization completed, ENE= -.10622198E+05 RMS= 0.174941E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0725E+04 1.7325E+01 1.1503E+02 C 1596 BOND = 1414.8307 ANGLE = 3804.3976 DIHED = 5398.0516 VDWAALS = -3931.4030 EEL = -35083.1175 EGB = -7603.4221 1-4 VDW = 1783.4265 1-4 EEL = 23309.7578 RESTRAINT = 0.0000 ESURF = 182.5151 minimization completed, ENE= -.10724963E+05 RMS= 0.173247E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0718E+04 1.7242E+01 1.1470E+02 CD 6794 BOND = 1400.3569 ANGLE = 3820.4369 DIHED = 5396.6987 VDWAALS = -3938.9139 EEL = -35012.1803 EGB = -7584.6305 1-4 VDW = 1784.8561 1-4 EEL = 23233.6316 RESTRAINT = 0.0000 ESURF = 181.2760 minimization completed, ENE= -.10718469E+05 RMS= 0.172424E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0735E+04 1.7363E+01 1.1617E+02 C 6113 BOND = 1451.3713 ANGLE = 3729.9434 DIHED = 5389.4075 VDWAALS = -3896.0871 EEL = -35105.5123 EGB = -7509.8402 1-4 VDW = 1764.3208 1-4 EEL = 23259.8327 RESTRAINT = 0.0000 ESURF = 181.7648 minimization completed, ENE= -.10734799E+05 RMS= 0.173630E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0738E+04 1.7238E+01 1.0749E+02 CA 7619 BOND = 1375.5984 ANGLE = 3753.0350 DIHED = 5412.1566 VDWAALS = -3886.1987 EEL = -35172.0100 EGB = -7538.8107 1-4 VDW = 1803.5881 1-4 EEL = 23331.0985 RESTRAINT = 0.0000 ESURF = 183.0942 minimization completed, ENE= -.10738449E+05 RMS= 0.172380E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0823E+04 1.7265E+01 1.1049E+02 C 2378 BOND = 1391.0964 ANGLE = 3820.9261 DIHED = 5408.3222 VDWAALS = -3998.2414 EEL = -35049.7797 EGB = -7505.5025 1-4 VDW = 1765.5876 1-4 EEL = 23163.6187 RESTRAINT = 0.0000 ESURF = 180.6968 minimization completed, ENE= -.10823276E+05 RMS= 0.172650E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0696E+04 1.7529E+01 1.2907E+02 C 6885 BOND = 1432.2719 ANGLE = 3812.7049 DIHED = 5378.3912 VDWAALS = -3918.4037 EEL = -35104.9485 EGB = -7529.7874 1-4 VDW = 1799.0869 1-4 EEL = 23253.0160 RESTRAINT = 0.0000 ESURF = 181.9755 minimization completed, ENE= -.10695693E+05 RMS= 0.175290E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0599E+04 1.7423E+01 1.1350E+02 OD1 4707 BOND = 1452.8281 ANGLE = 3840.4891 DIHED = 5427.8308 VDWAALS = -3970.4582 EEL = -35216.3665 EGB = -7421.9614 1-4 VDW = 1802.2452 1-4 EEL = 23305.7608 RESTRAINT = 0.0000 ESURF = 180.3534 minimization completed, ENE= -.10599279E+05 RMS= 0.174232E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0887E+04 1.6912E+01 1.3014E+02 CA 5626 BOND = 1369.5085 ANGLE = 3729.4849 DIHED = 5391.4495 VDWAALS = -3935.2364 EEL = -35171.3355 EGB = -7501.5282 1-4 VDW = 1785.6772 1-4 EEL = 23263.6903 RESTRAINT = 0.0000 ESURF = 181.5868 minimization completed, ENE= -.10886703E+05 RMS= 0.169123E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0709E+04 1.7307E+01 1.2377E+02 C 1502 BOND = 1402.0064 ANGLE = 3817.5385 DIHED = 5422.1116 VDWAALS = -3928.2146 EEL = -35116.4994 EGB = -7549.1878 1-4 VDW = 1802.4319 1-4 EEL = 23258.7134 RESTRAINT = 0.0000 ESURF = 181.6976 minimization completed, ENE= -.10709402E+05 RMS= 0.173069E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0815E+04 1.7281E+01 1.2657E+02 C 5557 BOND = 1408.3028 ANGLE = 3695.3427 DIHED = 5377.9139 VDWAALS = -3903.2465 EEL = -35228.0497 EGB = -7440.0199 1-4 VDW = 1801.7721 1-4 EEL = 23292.9024 RESTRAINT = 0.0000 ESURF = 179.7186 minimization completed, ENE= -.10815364E+05 RMS= 0.172813E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0795E+04 1.7233E+01 1.1515E+02 N 5685 BOND = 1390.1125 ANGLE = 3777.4941 DIHED = 5387.0020 VDWAALS = -3954.6604 EEL = -35093.5312 EGB = -7538.2252 1-4 VDW = 1784.7960 1-4 EEL = 23272.6258 RESTRAINT = 0.0000 ESURF = 179.8052 minimization completed, ENE= -.10794581E+05 RMS= 0.172326E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0766E+04 1.7348E+01 1.2066E+02 C 2330 BOND = 1365.7172 ANGLE = 3761.0818 DIHED = 5408.7431 VDWAALS = -3882.9941 EEL = -35255.9538 EGB = -7508.7161 1-4 VDW = 1829.3822 1-4 EEL = 23336.7911 RESTRAINT = 0.0000 ESURF = 179.7631 minimization completed, ENE= -.10766185E+05 RMS= 0.173484E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0731E+04 1.7477E+01 1.1695E+02 N 1511 BOND = 1415.0011 ANGLE = 3836.4952 DIHED = 5418.6646 VDWAALS = -4005.4401 EEL = -35162.9447 EGB = -7486.2747 1-4 VDW = 1791.8631 1-4 EEL = 23282.4963 RESTRAINT = 0.0000 ESURF = 178.8752 minimization completed, ENE= -.10731264E+05 RMS= 0.174769E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0757E+04 1.7361E+01 1.2673E+02 C 5475 BOND = 1451.7388 ANGLE = 3695.4710 DIHED = 5365.0245 VDWAALS = -3883.2105 EEL = -35342.3884 EGB = -7403.6616 1-4 VDW = 1840.0747 1-4 EEL = 23339.3296 RESTRAINT = 0.0000 ESURF = 180.7597 minimization completed, ENE= -.10756862E+05 RMS= 0.173614E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0715E+04 1.7203E+01 1.1351E+02 CZ 7561 BOND = 1372.2685 ANGLE = 3759.6361 DIHED = 5441.9092 VDWAALS = -3956.7627 EEL = -35154.4324 EGB = -7462.3669 1-4 VDW = 1808.2809 1-4 EEL = 23294.5434 RESTRAINT = 0.0000 ESURF = 181.7375 minimization completed, ENE= -.10715186E+05 RMS= 0.172029E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0792E+04 1.7305E+01 1.1367E+02 C 2030 BOND = 1371.6136 ANGLE = 3737.2356 DIHED = 5433.9479 VDWAALS = -3929.9823 EEL = -35409.6323 EGB = -7312.0802 1-4 VDW = 1795.9032 1-4 EEL = 23341.5084 RESTRAINT = 0.0000 ESURF = 179.2113 minimization completed, ENE= -.10792275E+05 RMS= 0.173047E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0774E+04 1.7215E+01 1.1013E+02 C 7452 BOND = 1397.0235 ANGLE = 3738.8990 DIHED = 5409.9579 VDWAALS = -3860.4832 EEL = -35393.9715 EGB = -7321.2914 1-4 VDW = 1803.5182 1-4 EEL = 23271.7821 RESTRAINT = 0.0000 ESURF = 180.5092 minimization completed, ENE= -.10774056E+05 RMS= 0.172152E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0646E+04 1.7519E+01 1.3217E+02 CD 3751 BOND = 1408.2715 ANGLE = 3832.6800 DIHED = 5395.8400 VDWAALS = -3890.3503 EEL = -35153.4257 EGB = -7519.4624 1-4 VDW = 1814.2254 1-4 EEL = 23283.6120 RESTRAINT = 0.0000 ESURF = 183.0604 minimization completed, ENE= -.10645549E+05 RMS= 0.175189E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0763E+04 1.7549E+01 1.0588E+02 CG 2253 BOND = 1454.6829 ANGLE = 3745.1587 DIHED = 5389.4119 VDWAALS = -3863.1038 EEL = -35095.2706 EGB = -7583.9857 1-4 VDW = 1788.6395 1-4 EEL = 23217.6168 RESTRAINT = 0.0000 ESURF = 184.3388 minimization completed, ENE= -.10762512E+05 RMS= 0.175494E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0691E+04 1.7314E+01 1.2391E+02 C 4639 BOND = 1460.0847 ANGLE = 3729.2733 DIHED = 5497.2861 VDWAALS = -3906.0897 EEL = -35165.8873 EGB = -7528.0890 1-4 VDW = 1779.3129 1-4 EEL = 23259.5707 RESTRAINT = 0.0000 ESURF = 183.6092 minimization completed, ENE= -.10690929E+05 RMS= 0.173139E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 718.46 ( 7.75% of Gen B) | Calc gb diag 5525.02 (59.62% of Gen B) | Calc gb off-diag 3023.07 (32.62% of Gen B) | Gen Born time 9266.56 (100.0% of Nonbo) | Nonbond force 9266.56 (100.0% of Force) | Bond/Angle/Dihedral 6.23 ( 0.07% of Force) | Other 0.51 ( 0.01% of Force) | Force time 9273.30 (100.0% of Runmd) | Runmd Time 9273.30 (98.86% of Total) | Other 106.62 ( 1.14% of Total) | Total time 9379.94 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 19:12:37.101 on 10/19/2010 | Setup done at 19:12:41.330 on 10/19/2010 | Run done at 21:48:57.040 on 10/19/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/19/2010 at 19:12:38 [-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 -1.0696E+04 1.7459E+01 1.1641E+02 C 5456 BOND = 1415.7892 ANGLE = 3881.7026 DIHED = 5415.3437 VDWAALS = -3934.5289 EEL = -35300.6395 EGB = -7396.2175 1-4 VDW = 1794.1412 1-4 EEL = 23249.2367 RESTRAINT = 0.0000 ESURF = 178.7837 minimization completed, ENE= -.10696389E+05 RMS= 0.174585E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0783E+04 1.7343E+01 1.0734E+02 C 4374 BOND = 1450.6461 ANGLE = 3762.4328 DIHED = 5419.9058 VDWAALS = -3904.1434 EEL = -35467.7716 EGB = -7308.6805 1-4 VDW = 1794.2049 1-4 EEL = 23291.9206 RESTRAINT = 0.0000 ESURF = 178.5343 minimization completed, ENE= -.10782951E+05 RMS= 0.173426E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0767E+04 1.7240E+01 9.9855E+01 C 1862 BOND = 1452.3963 ANGLE = 3677.9463 DIHED = 5462.3040 VDWAALS = -3989.2005 EEL = -35414.2358 EGB = -7253.6918 1-4 VDW = 1804.2516 1-4 EEL = 23315.6820 RESTRAINT = 0.0000 ESURF = 177.8875 minimization completed, ENE= -.10766660E+05 RMS= 0.172398E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0762E+04 1.7327E+01 1.2129E+02 C 1576 BOND = 1414.8462 ANGLE = 3744.2549 DIHED = 5413.2220 VDWAALS = -3917.2940 EEL = -35398.0194 EGB = -7296.8691 1-4 VDW = 1805.0377 1-4 EEL = 23294.8742 RESTRAINT = 0.0000 ESURF = 177.7955 minimization completed, ENE= -.10762152E+05 RMS= 0.173270E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0724E+04 1.7358E+01 1.1236E+02 CZ 173 BOND = 1478.4849 ANGLE = 3731.0240 DIHED = 5379.1248 VDWAALS = -3908.7361 EEL = -35399.3370 EGB = -7375.0019 1-4 VDW = 1835.1660 1-4 EEL = 23355.9509 RESTRAINT = 0.0000 ESURF = 179.3095 minimization completed, ENE= -.10724015E+05 RMS= 0.173579E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0711E+04 1.7539E+01 1.1356E+02 CE1 665 BOND = 1462.1803 ANGLE = 3711.4859 DIHED = 5454.3084 VDWAALS = -3909.9487 EEL = -35425.3917 EGB = -7313.6745 1-4 VDW = 1836.4652 1-4 EEL = 23294.0804 RESTRAINT = 0.0000 ESURF = 179.2232 minimization completed, ENE= -.10711271E+05 RMS= 0.175387E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0905E+04 1.7255E+01 1.1178E+02 CG 4904 BOND = 1424.5431 ANGLE = 3714.3068 DIHED = 5398.7214 VDWAALS = -3958.9903 EEL = -35224.6713 EGB = -7425.5531 1-4 VDW = 1776.9450 1-4 EEL = 23210.2839 RESTRAINT = 0.0000 ESURF = 179.1034 minimization completed, ENE= -.10905311E+05 RMS= 0.172553E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0766E+04 1.7069E+01 1.0900E+02 CA 796 BOND = 1369.3201 ANGLE = 3746.4678 DIHED = 5427.6771 VDWAALS = -3936.0490 EEL = -35178.4440 EGB = -7473.7621 1-4 VDW = 1815.4852 1-4 EEL = 23281.7302 RESTRAINT = 0.0000 ESURF = 181.5081 minimization completed, ENE= -.10766067E+05 RMS= 0.170693E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0768E+04 1.7353E+01 1.0478E+02 CB 3745 BOND = 1449.2157 ANGLE = 3727.4770 DIHED = 5417.6364 VDWAALS = -3904.4729 EEL = -35347.9498 EGB = -7384.0185 1-4 VDW = 1797.3164 1-4 EEL = 23296.0421 RESTRAINT = 0.0000 ESURF = 180.9129 minimization completed, ENE= -.10767841E+05 RMS= 0.173532E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0837E+04 1.7281E+01 1.0546E+02 CZ 7109 BOND = 1390.7637 ANGLE = 3737.8876 DIHED = 5378.3624 VDWAALS = -3934.8240 EEL = -35418.0591 EGB = -7271.9198 1-4 VDW = 1810.0059 1-4 EEL = 23291.6126 RESTRAINT = 0.0000 ESURF = 178.7716 minimization completed, ENE= -.10837399E+05 RMS= 0.172813E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0804E+04 1.7468E+01 1.1938E+02 C 3359 BOND = 1433.0936 ANGLE = 3668.5079 DIHED = 5409.7990 VDWAALS = -3922.3366 EEL = -35391.6005 EGB = -7296.5077 1-4 VDW = 1815.8365 1-4 EEL = 23301.5702 RESTRAINT = 0.0000 ESURF = 177.4858 minimization completed, ENE= -.10804152E+05 RMS= 0.174685E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0733E+04 1.7236E+01 1.0969E+02 CZ 1000 BOND = 1431.1938 ANGLE = 3762.4155 DIHED = 5454.4661 VDWAALS = -3897.0379 EEL = -35406.2107 EGB = -7314.5186 1-4 VDW = 1793.5176 1-4 EEL = 23263.3273 RESTRAINT = 0.0000 ESURF = 179.9869 minimization completed, ENE= -.10732860E+05 RMS= 0.172362E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0768E+04 1.7383E+01 1.1202E+02 C 2285 BOND = 1401.4933 ANGLE = 3746.0220 DIHED = 5451.2394 VDWAALS = -3932.3347 EEL = -35518.7760 EGB = -7242.8884 1-4 VDW = 1782.4512 1-4 EEL = 23367.6758 RESTRAINT = 0.0000 ESURF = 177.4952 minimization completed, ENE= -.10767622E+05 RMS= 0.173830E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0741E+04 1.7498E+01 1.2688E+02 N 2622 BOND = 1460.8312 ANGLE = 3709.5264 DIHED = 5420.2055 VDWAALS = -3956.3253 EEL = -35334.5710 EGB = -7320.2769 1-4 VDW = 1783.2812 1-4 EEL = 23319.4337 RESTRAINT = 0.0000 ESURF = 177.3441 minimization completed, ENE= -.10740551E+05 RMS= 0.174983E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0698E+04 1.7372E+01 1.1719E+02 CD 5504 BOND = 1458.3468 ANGLE = 3765.4177 DIHED = 5438.0862 VDWAALS = -3933.8286 EEL = -35290.3087 EGB = -7366.4902 1-4 VDW = 1796.8766 1-4 EEL = 23253.8974 RESTRAINT = 0.0000 ESURF = 180.1758 minimization completed, ENE= -.10697827E+05 RMS= 0.173717E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0832E+04 1.7216E+01 1.2125E+02 C 6526 BOND = 1415.9758 ANGLE = 3725.7183 DIHED = 5421.9593 VDWAALS = -3932.4254 EEL = -35373.3032 EGB = -7303.9661 1-4 VDW = 1795.3001 1-4 EEL = 23239.0546 RESTRAINT = 0.0000 ESURF = 180.1254 minimization completed, ENE= -.10831561E+05 RMS= 0.172163E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0800E+04 1.7068E+01 1.2157E+02 C 3999 BOND = 1362.6000 ANGLE = 3791.2788 DIHED = 5414.1876 VDWAALS = -3955.0517 EEL = -35485.2457 EGB = -7234.3502 1-4 VDW = 1797.5151 1-4 EEL = 23329.0280 RESTRAINT = 0.0000 ESURF = 179.9119 minimization completed, ENE= -.10800126E+05 RMS= 0.170685E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0700E+04 1.7406E+01 1.1420E+02 C 7668 BOND = 1428.0888 ANGLE = 3844.8155 DIHED = 5451.7086 VDWAALS = -3976.4225 EEL = -35425.4438 EGB = -7284.5366 1-4 VDW = 1818.4994 1-4 EEL = 23265.5358 RESTRAINT = 0.0000 ESURF = 177.7562 minimization completed, ENE= -.10699999E+05 RMS= 0.174061E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0720E+04 1.7279E+01 1.1079E+02 C 2499 BOND = 1420.3212 ANGLE = 3780.1544 DIHED = 5458.7883 VDWAALS = -3894.1627 EEL = -35409.6749 EGB = -7358.4021 1-4 VDW = 1812.0862 1-4 EEL = 23290.2361 RESTRAINT = 0.0000 ESURF = 180.7066 minimization completed, ENE= -.10719947E+05 RMS= 0.172794E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0767E+04 1.7320E+01 1.3273E+02 C 2393 BOND = 1386.1663 ANGLE = 3753.1527 DIHED = 5422.2901 VDWAALS = -3923.2333 EEL = -35294.8952 EGB = -7433.8807 1-4 VDW = 1791.9938 1-4 EEL = 23351.6467 RESTRAINT = 0.0000 ESURF = 180.0796 minimization completed, ENE= -.10766680E+05 RMS= 0.173199E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0828E+04 1.7241E+01 9.7685E+01 C 2782 BOND = 1451.7438 ANGLE = 3714.4670 DIHED = 5394.3141 VDWAALS = -3943.3447 EEL = -35196.3897 EGB = -7508.7025 1-4 VDW = 1769.8409 1-4 EEL = 23308.7787 RESTRAINT = 0.0000 ESURF = 181.4391 minimization completed, ENE= -.10827853E+05 RMS= 0.172413E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0733E+04 1.7335E+01 1.1575E+02 N 5287 BOND = 1403.2838 ANGLE = 3791.4989 DIHED = 5412.4320 VDWAALS = -3914.9921 EEL = -35223.9437 EGB = -7435.1567 1-4 VDW = 1781.3458 1-4 EEL = 23272.3848 RESTRAINT = 0.0000 ESURF = 180.0128 minimization completed, ENE= -.10733135E+05 RMS= 0.173345E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0696E+04 1.7416E+01 1.2156E+02 CG 6398 BOND = 1440.3514 ANGLE = 3772.9893 DIHED = 5422.1824 VDWAALS = -3930.1511 EEL = -35374.3414 EGB = -7377.0891 1-4 VDW = 1800.5928 1-4 EEL = 23367.8479 RESTRAINT = 0.0000 ESURF = 181.1361 minimization completed, ENE= -.10696482E+05 RMS= 0.174165E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0824E+04 1.7162E+01 1.1923E+02 C 1528 BOND = 1407.8029 ANGLE = 3696.9877 DIHED = 5419.5091 VDWAALS = -3935.4619 EEL = -35406.3766 EGB = -7315.7508 1-4 VDW = 1791.0792 1-4 EEL = 23339.1116 RESTRAINT = 0.0000 ESURF = 179.1030 minimization completed, ENE= -.10823996E+05 RMS= 0.171620E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0814E+04 1.7327E+01 1.2480E+02 CG 6506 BOND = 1403.3899 ANGLE = 3727.0662 DIHED = 5434.0715 VDWAALS = -3950.5236 EEL = -35437.8382 EGB = -7264.2957 1-4 VDW = 1813.9329 1-4 EEL = 23282.6531 RESTRAINT = 0.0000 ESURF = 177.5387 minimization completed, ENE= -.10814005E+05 RMS= 0.173273E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0787E+04 1.7329E+01 1.1141E+02 CD 3135 BOND = 1447.6795 ANGLE = 3727.3419 DIHED = 5384.0280 VDWAALS = -3963.9217 EEL = -35396.5018 EGB = -7290.8555 1-4 VDW = 1826.1064 1-4 EEL = 23301.8662 RESTRAINT = 0.0000 ESURF = 177.0455 minimization completed, ENE= -.10787212E+05 RMS= 0.173291E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0723E+04 1.7469E+01 1.0027E+02 CA 3176 BOND = 1420.1075 ANGLE = 3791.8682 DIHED = 5398.2604 VDWAALS = -3909.5898 EEL = -35207.8773 EGB = -7439.4040 1-4 VDW = 1804.6742 1-4 EEL = 23239.6541 RESTRAINT = 0.0000 ESURF = 179.3495 minimization completed, ENE= -.10722957E+05 RMS= 0.174689E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0791E+04 1.7251E+01 9.7039E+01 C 5006 BOND = 1417.6337 ANGLE = 3746.7970 DIHED = 5385.8746 VDWAALS = -3971.0681 EEL = -35501.1345 EGB = -7225.6975 1-4 VDW = 1819.8531 1-4 EEL = 23358.5777 RESTRAINT = 0.0000 ESURF = 177.8462 minimization completed, ENE= -.10791318E+05 RMS= 0.172510E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0841E+04 1.7361E+01 1.2012E+02 CD 5184 BOND = 1413.7842 ANGLE = 3773.8919 DIHED = 5393.1333 VDWAALS = -3896.1973 EEL = -35435.6034 EGB = -7325.2442 1-4 VDW = 1813.9204 1-4 EEL = 23240.1984 RESTRAINT = 0.0000 ESURF = 180.7366 minimization completed, ENE= -.10841380E+05 RMS= 0.173613E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0854E+04 1.7423E+01 1.1592E+02 C 1059 BOND = 1446.8823 ANGLE = 3643.5837 DIHED = 5389.8808 VDWAALS = -3949.4087 EEL = -35368.0182 EGB = -7400.2205 1-4 VDW = 1816.8914 1-4 EEL = 23386.5320 RESTRAINT = 0.0000 ESURF = 179.4943 minimization completed, ENE= -.10854383E+05 RMS= 0.174228E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0883E+04 1.7211E+01 1.2204E+02 C 1297 BOND = 1384.1438 ANGLE = 3659.5563 DIHED = 5391.4457 VDWAALS = -4001.6468 EEL = -35070.8423 EGB = -7608.9734 1-4 VDW = 1808.9559 1-4 EEL = 23374.2013 RESTRAINT = 0.0000 ESURF = 180.3525 minimization completed, ENE= -.10882807E+05 RMS= 0.172114E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0705E+04 1.7558E+01 1.2020E+02 C 5579 BOND = 1429.3738 ANGLE = 3802.9303 DIHED = 5402.2555 VDWAALS = -3957.5613 EEL = -34974.7080 EGB = -7626.3430 1-4 VDW = 1778.7813 1-4 EEL = 23260.2113 RESTRAINT = 0.0000 ESURF = 180.2069 minimization completed, ENE= -.10704853E+05 RMS= 0.175581E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0826E+04 1.7181E+01 1.0780E+02 CG 2253 BOND = 1424.9519 ANGLE = 3727.5404 DIHED = 5423.1075 VDWAALS = -3932.4561 EEL = -35106.9628 EGB = -7506.2740 1-4 VDW = 1766.7402 1-4 EEL = 23197.3474 RESTRAINT = 0.0000 ESURF = 180.1826 minimization completed, ENE= -.10825823E+05 RMS= 0.171811E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0778E+04 1.7053E+01 1.0957E+02 CD 5041 BOND = 1366.1950 ANGLE = 3820.3104 DIHED = 5399.6371 VDWAALS = -3954.6461 EEL = -35074.6869 EGB = -7615.6073 1-4 VDW = 1816.7011 1-4 EEL = 23283.4917 RESTRAINT = 0.0000 ESURF = 180.6490 minimization completed, ENE= -.10777956E+05 RMS= 0.170532E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0597E+04 1.7224E+01 1.1492E+02 N 1744 BOND = 1441.1012 ANGLE = 3796.1997 DIHED = 5467.9060 VDWAALS = -3965.9057 EEL = -35073.3051 EGB = -7510.6354 1-4 VDW = 1803.5897 1-4 EEL = 23264.2960 RESTRAINT = 0.0000 ESURF = 180.1005 minimization completed, ENE= -.10596653E+05 RMS= 0.172245E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0680E+04 1.7402E+01 1.2117E+02 CG 7797 BOND = 1416.0990 ANGLE = 3794.6878 DIHED = 5449.7100 VDWAALS = -3940.2926 EEL = -35213.3810 EGB = -7500.8802 1-4 VDW = 1808.2906 1-4 EEL = 23324.6882 RESTRAINT = 0.0000 ESURF = 180.8385 minimization completed, ENE= -.10680240E+05 RMS= 0.174016E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0673E+04 1.7278E+01 1.1507E+02 C 3829 BOND = 1442.5600 ANGLE = 3744.1991 DIHED = 5434.5701 VDWAALS = -3941.3182 EEL = -35028.5001 EGB = -7632.4464 1-4 VDW = 1795.4130 1-4 EEL = 23332.2623 RESTRAINT = 0.0000 ESURF = 179.8963 minimization completed, ENE= -.10673364E+05 RMS= 0.172781E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0759E+04 1.7200E+01 1.2191E+02 CG 6506 BOND = 1391.5129 ANGLE = 3740.1038 DIHED = 5432.9592 VDWAALS = -3913.8433 EEL = -35077.0969 EGB = -7612.1001 1-4 VDW = 1812.6136 1-4 EEL = 23285.8913 RESTRAINT = 0.0000 ESURF = 180.6236 minimization completed, ENE= -.10759336E+05 RMS= 0.171999E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0734E+04 1.7403E+01 1.3063E+02 C 2537 BOND = 1409.0255 ANGLE = 3713.3640 DIHED = 5406.7384 VDWAALS = -3899.6424 EEL = -35178.5496 EGB = -7557.4583 1-4 VDW = 1841.2961 1-4 EEL = 23350.7368 RESTRAINT = 0.0000 ESURF = 180.3059 minimization completed, ENE= -.10734184E+05 RMS= 0.174033E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0738E+04 1.7606E+01 1.2538E+02 N 1121 BOND = 1426.2535 ANGLE = 3820.4616 DIHED = 5392.4020 VDWAALS = -3982.8292 EEL = -35151.1178 EGB = -7529.1225 1-4 VDW = 1795.0266 1-4 EEL = 23311.3977 RESTRAINT = 0.0000 ESURF = 179.7692 minimization completed, ENE= -.10737759E+05 RMS= 0.176056E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0623E+04 1.7461E+01 1.1637E+02 CG 2050 BOND = 1378.3981 ANGLE = 3820.9881 DIHED = 5405.4389 VDWAALS = -3900.4946 EEL = -35188.2771 EGB = -7582.3587 1-4 VDW = 1835.8127 1-4 EEL = 23426.2890 RESTRAINT = 0.0000 ESURF = 180.8160 minimization completed, ENE= -.10623388E+05 RMS= 0.174609E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0855E+04 1.7228E+01 1.1631E+02 C 7788 BOND = 1384.2900 ANGLE = 3703.8257 DIHED = 5388.1545 VDWAALS = -3971.2686 EEL = -35097.2078 EGB = -7508.2388 1-4 VDW = 1812.5676 1-4 EEL = 23253.5695 RESTRAINT = 0.0000 ESURF = 179.1447 minimization completed, ENE= -.10855163E+05 RMS= 0.172277E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0740E+04 1.7369E+01 1.3019E+02 CG 52 BOND = 1403.5418 ANGLE = 3777.7982 DIHED = 5390.2334 VDWAALS = -3975.3468 EEL = -35053.4994 EGB = -7571.1030 1-4 VDW = 1785.3656 1-4 EEL = 23323.3544 RESTRAINT = 0.0000 ESURF = 180.0264 minimization completed, ENE= -.10739629E+05 RMS= 0.173694E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0811E+04 1.7061E+01 1.2173E+02 CD 4507 BOND = 1391.1856 ANGLE = 3668.3366 DIHED = 5380.4902 VDWAALS = -3930.4943 EEL = -35066.8236 EGB = -7574.3957 1-4 VDW = 1836.3495 1-4 EEL = 23304.4122 RESTRAINT = 0.0000 ESURF = 179.5716 minimization completed, ENE= -.10811368E+05 RMS= 0.170611E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0678E+04 1.7593E+01 1.2261E+02 C 285 BOND = 1410.1650 ANGLE = 3822.9672 DIHED = 5458.7243 VDWAALS = -3935.3043 EEL = -34999.9961 EGB = -7721.2036 1-4 VDW = 1783.8053 1-4 EEL = 23322.8958 RESTRAINT = 0.0000 ESURF = 180.0030 minimization completed, ENE= -.10677943E+05 RMS= 0.175934E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0832E+04 1.7157E+01 1.4345E+02 CG 3293 BOND = 1385.5618 ANGLE = 3663.6260 DIHED = 5376.2610 VDWAALS = -3921.7353 EEL = -35273.4771 EGB = -7342.1525 1-4 VDW = 1796.6412 1-4 EEL = 23304.5907 RESTRAINT = 0.0000 ESURF = 179.1769 minimization completed, ENE= -.10831507E+05 RMS= 0.171566E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0774E+04 1.7295E+01 1.2043E+02 CA 3176 BOND = 1446.8679 ANGLE = 3700.2077 DIHED = 5398.8334 VDWAALS = -3924.9659 EEL = -35184.2887 EGB = -7493.8264 1-4 VDW = 1813.3537 1-4 EEL = 23289.1266 RESTRAINT = 0.0000 ESURF = 180.7674 minimization completed, ENE= -.10773924E+05 RMS= 0.172951E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0718E+04 1.7568E+01 1.2760E+02 C 113 BOND = 1430.0000 ANGLE = 3831.1671 DIHED = 5351.1399 VDWAALS = -3940.8301 EEL = -35381.1826 EGB = -7351.7401 1-4 VDW = 1825.7873 1-4 EEL = 23339.9401 RESTRAINT = 0.0000 ESURF = 178.1462 minimization completed, ENE= -.10717572E+05 RMS= 0.175678E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0697E+04 1.7648E+01 1.2116E+02 CA 488 BOND = 1461.7013 ANGLE = 3860.2946 DIHED = 5406.8611 VDWAALS = -3948.8140 EEL = -35308.6442 EGB = -7377.9135 1-4 VDW = 1785.1737 1-4 EEL = 23245.7431 RESTRAINT = 0.0000 ESURF = 178.6239 minimization completed, ENE= -.10696974E+05 RMS= 0.176476E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0723E+04 1.7099E+01 1.0483E+02 CD 6463 BOND = 1390.7914 ANGLE = 3753.0741 DIHED = 5407.3367 VDWAALS = -3933.1374 EEL = -35278.7375 EGB = -7290.6796 1-4 VDW = 1820.3490 1-4 EEL = 23229.1603 RESTRAINT = 0.0000 ESURF = 178.3703 minimization completed, ENE= -.10723473E+05 RMS= 0.170988E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 722.69 ( 7.74% of Gen B) | Calc gb diag 5574.97 (59.68% of Gen B) | Calc gb off-diag 3044.27 (32.59% of Gen B) | Gen Born time 9341.93 (100.0% of Nonbo) | Nonbond force 9341.93 (99.90% of Force) | Bond/Angle/Dihedral 9.42 ( 0.10% of Force) | Force time 9351.36 (100.0% of Runmd) | Runmd Time 9351.36 (98.91% of Total) | Other 103.41 ( 1.09% of Total) | Total time 9454.79 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 19:12:37.205 on 10/19/2010 | Setup done at 19:12:40.002 on 10/19/2010 | Run done at 21:50:11.995 on 10/19/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/19/2010 at 19:12:37 [-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 -1.0783E+04 1.7164E+01 1.1420E+02 CZ 2900 BOND = 1384.4909 ANGLE = 3749.4758 DIHED = 5427.5432 VDWAALS = -3903.0705 EEL = -35248.0821 EGB = -7491.3621 1-4 VDW = 1805.1146 1-4 EEL = 23312.6929 RESTRAINT = 0.0000 ESURF = 180.4629 minimization completed, ENE= -.10782734E+05 RMS= 0.171639E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0823E+04 1.7328E+01 1.2315E+02 CG 4342 BOND = 1407.7389 ANGLE = 3722.2186 DIHED = 5386.0862 VDWAALS = -3904.3865 EEL = -35185.5322 EGB = -7569.5911 1-4 VDW = 1803.0314 1-4 EEL = 23337.9199 RESTRAINT = 0.0000 ESURF = 179.3328 minimization completed, ENE= -.10823182E+05 RMS= 0.173278E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0848E+04 1.7291E+01 1.0966E+02 C 1648 BOND = 1426.7395 ANGLE = 3703.4575 DIHED = 5429.2344 VDWAALS = -3970.2310 EEL = -35421.0173 EGB = -7310.5939 1-4 VDW = 1786.9969 1-4 EEL = 23329.6770 RESTRAINT = 0.0000 ESURF = 177.7015 minimization completed, ENE= -.10848035E+05 RMS= 0.172905E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0984E+04 1.6950E+01 1.1508E+02 CA 612 BOND = 1375.1579 ANGLE = 3638.9233 DIHED = 5405.4245 VDWAALS = -3971.5518 EEL = -35292.4006 EGB = -7379.3511 1-4 VDW = 1789.9763 1-4 EEL = 23271.6957 RESTRAINT = 0.0000 ESURF = 178.3645 minimization completed, ENE= -.10983761E+05 RMS= 0.169502E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0745E+04 1.7264E+01 1.1613E+02 CA 2930 BOND = 1397.4417 ANGLE = 3730.0405 DIHED = 5456.4856 VDWAALS = -3956.1258 EEL = -35303.7362 EGB = -7364.9120 1-4 VDW = 1816.7176 1-4 EEL = 23302.3242 RESTRAINT = 0.0000 ESURF = 177.2552 minimization completed, ENE= -.10744509E+05 RMS= 0.172637E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0732E+04 1.7353E+01 1.1067E+02 C4 7871 BOND = 1421.2463 ANGLE = 3754.4414 DIHED = 5412.1136 VDWAALS = -3962.6359 EEL = -35161.3527 EGB = -7462.1265 1-4 VDW = 1815.2767 1-4 EEL = 23271.6688 RESTRAINT = 0.0000 ESURF = 179.4542 minimization completed, ENE= -.10731914E+05 RMS= 0.173533E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0708E+04 1.7067E+01 1.0923E+02 C 7074 BOND = 1422.9331 ANGLE = 3822.4248 DIHED = 5450.4733 VDWAALS = -3944.5787 EEL = -35218.3155 EGB = -7552.1881 1-4 VDW = 1795.7382 1-4 EEL = 23336.4509 RESTRAINT = 0.0000 ESURF = 179.2883 minimization completed, ENE= -.10707774E+05 RMS= 0.170673E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0808E+04 1.7408E+01 1.0987E+02 C 2432 BOND = 1426.1538 ANGLE = 3696.0763 DIHED = 5404.5070 VDWAALS = -3920.3556 EEL = -35524.8282 EGB = -7269.1994 1-4 VDW = 1801.5988 1-4 EEL = 23400.5526 RESTRAINT = 0.0000 ESURF = 177.5648 minimization completed, ENE= -.10807930E+05 RMS= 0.174076E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0737E+04 1.7320E+01 1.1716E+02 C 5069 BOND = 1482.7494 ANGLE = 3731.4980 DIHED = 5461.4523 VDWAALS = -3942.3200 EEL = -35264.6656 EGB = -7346.0757 1-4 VDW = 1794.2979 1-4 EEL = 23167.3932 RESTRAINT = 0.0000 ESURF = 178.9503 minimization completed, ENE= -.10736720E+05 RMS= 0.173198E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0830E+04 1.7335E+01 1.2775E+02 C 964 BOND = 1411.3524 ANGLE = 3727.2578 DIHED = 5387.4874 VDWAALS = -3927.9774 EEL = -35280.4743 EGB = -7474.2001 1-4 VDW = 1807.1636 1-4 EEL = 23340.9889 RESTRAINT = 0.0000 ESURF = 178.4991 minimization completed, ENE= -.10829903E+05 RMS= 0.173352E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0916E+04 1.7098E+01 1.3606E+02 CG 2852 BOND = 1413.7952 ANGLE = 3666.3021 DIHED = 5404.3695 VDWAALS = -3938.3436 EEL = -35340.2711 EGB = -7406.3657 1-4 VDW = 1802.9594 1-4 EEL = 23301.7039 RESTRAINT = 0.0000 ESURF = 179.5352 minimization completed, ENE= -.10916315E+05 RMS= 0.170977E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0774E+04 1.7274E+01 1.1520E+02 C 6206 BOND = 1398.3330 ANGLE = 3799.0093 DIHED = 5381.7697 VDWAALS = -3916.9303 EEL = -35221.9244 EGB = -7512.2240 1-4 VDW = 1802.2474 1-4 EEL = 23316.2889 RESTRAINT = 0.0000 ESURF = 179.0621 minimization completed, ENE= -.10774368E+05 RMS= 0.172739E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0923E+04 1.7115E+01 1.1317E+02 C 7715 BOND = 1401.5391 ANGLE = 3674.6780 DIHED = 5369.9474 VDWAALS = -3880.6126 EEL = -35226.4931 EGB = -7419.0516 1-4 VDW = 1786.8576 1-4 EEL = 23190.5976 RESTRAINT = 0.0000 ESURF = 179.5773 minimization completed, ENE= -.10922960E+05 RMS= 0.171146E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0789E+04 1.7302E+01 1.1809E+02 C 2064 BOND = 1440.0005 ANGLE = 3773.1530 DIHED = 5435.9211 VDWAALS = -3978.3339 EEL = -35089.9414 EGB = -7545.8019 1-4 VDW = 1791.5245 1-4 EEL = 23204.3225 RESTRAINT = 0.0000 ESURF = 180.1883 minimization completed, ENE= -.10788967E+05 RMS= 0.173018E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0811E+04 1.7223E+01 1.1367E+02 C 7511 BOND = 1401.6353 ANGLE = 3760.2855 DIHED = 5415.5732 VDWAALS = -3896.7147 EEL = -35262.1834 EGB = -7384.1607 1-4 VDW = 1784.0466 1-4 EEL = 23192.8369 RESTRAINT = 0.0000 ESURF = 177.3007 minimization completed, ENE= -.10811381E+05 RMS= 0.172229E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0743E+04 1.7171E+01 1.3805E+02 C 964 BOND = 1376.9034 ANGLE = 3719.3840 DIHED = 5461.5203 VDWAALS = -3956.8552 EEL = -35196.4438 EGB = -7458.9826 1-4 VDW = 1811.0671 1-4 EEL = 23322.9540 RESTRAINT = 0.0000 ESURF = 177.8276 minimization completed, ENE= -.10742625E+05 RMS= 0.171706E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0829E+04 1.7328E+01 1.3412E+02 C 6277 BOND = 1394.5075 ANGLE = 3768.3478 DIHED = 5426.4408 VDWAALS = -3935.3965 EEL = -35247.6109 EGB = -7483.6874 1-4 VDW = 1806.1209 1-4 EEL = 23263.8515 RESTRAINT = 0.0000 ESURF = 178.6439 minimization completed, ENE= -.10828783E+05 RMS= 0.173285E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0800E+04 1.7219E+01 1.2437E+02 C 6620 BOND = 1386.8706 ANGLE = 3755.7037 DIHED = 5418.8872 VDWAALS = -3878.5367 EEL = -35418.6333 EGB = -7365.5369 1-4 VDW = 1835.9587 1-4 EEL = 23285.6479 RESTRAINT = 0.0000 ESURF = 179.5518 minimization completed, ENE= -.10800087E+05 RMS= 0.172191E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0882E+04 1.7100E+01 1.1421E+02 C 3552 BOND = 1387.9847 ANGLE = 3656.4168 DIHED = 5414.7774 VDWAALS = -3956.7527 EEL = -35233.8084 EGB = -7477.3306 1-4 VDW = 1806.4344 1-4 EEL = 23341.3991 RESTRAINT = 0.0000 ESURF = 178.5681 minimization completed, ENE= -.10882311E+05 RMS= 0.171004E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0636E+04 1.7564E+01 1.0284E+02 CZ 6294 BOND = 1448.8774 ANGLE = 3767.7786 DIHED = 5446.8096 VDWAALS = -3916.3463 EEL = -35307.9737 EGB = -7374.8284 1-4 VDW = 1807.5622 1-4 EEL = 23314.3678 RESTRAINT = 0.0000 ESURF = 178.1363 minimization completed, ENE= -.10635616E+05 RMS= 0.175641E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0760E+04 1.7267E+01 1.1059E+02 C 6482 BOND = 1390.0193 ANGLE = 3777.4175 DIHED = 5426.1609 VDWAALS = -3930.0970 EEL = -35215.4875 EGB = -7467.5790 1-4 VDW = 1808.9274 1-4 EEL = 23272.5962 RESTRAINT = 0.0000 ESURF = 178.2739 minimization completed, ENE= -.10759768E+05 RMS= 0.172669E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0763E+04 1.7348E+01 1.2866E+02 C 6620 BOND = 1429.2797 ANGLE = 3755.6721 DIHED = 5426.2955 VDWAALS = -3936.4889 EEL = -35238.7495 EGB = -7475.3464 1-4 VDW = 1802.2030 1-4 EEL = 23295.2016 RESTRAINT = 0.0000 ESURF = 178.8134 minimization completed, ENE= -.10763119E+05 RMS= 0.173483E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0663E+04 1.7420E+01 1.2619E+02 C 2064 BOND = 1414.9607 ANGLE = 3783.0358 DIHED = 5501.9085 VDWAALS = -3924.3333 EEL = -35201.7356 EGB = -7431.1532 1-4 VDW = 1794.2785 1-4 EEL = 23221.9134 RESTRAINT = 0.0000 ESURF = 178.2549 minimization completed, ENE= -.10662870E+05 RMS= 0.174195E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0793E+04 1.7276E+01 1.1874E+02 CB 7707 BOND = 1445.3981 ANGLE = 3757.5934 DIHED = 5420.6895 VDWAALS = -3968.7631 EEL = -35161.6343 EGB = -7512.8966 1-4 VDW = 1790.1837 1-4 EEL = 23258.7024 RESTRAINT = 0.0000 ESURF = 177.9068 minimization completed, ENE= -.10792820E+05 RMS= 0.172764E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0831E+04 1.7410E+01 1.1866E+02 C 2432 BOND = 1414.0323 ANGLE = 3734.0032 DIHED = 5401.0033 VDWAALS = -3965.6716 EEL = -35095.9448 EGB = -7632.0733 1-4 VDW = 1801.9010 1-4 EEL = 23331.8307 RESTRAINT = 0.0000 ESURF = 179.8047 minimization completed, ENE= -.10831114E+05 RMS= 0.174096E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0808E+04 1.7253E+01 1.1160E+02 C 3384 BOND = 1381.3999 ANGLE = 3765.7792 DIHED = 5437.8990 VDWAALS = -3943.5034 EEL = -35180.3080 EGB = -7466.5089 1-4 VDW = 1787.6455 1-4 EEL = 23231.5516 RESTRAINT = 0.0000 ESURF = 178.1549 minimization completed, ENE= -.10807890E+05 RMS= 0.172534E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0783E+04 1.7245E+01 1.0868E+02 C 5434 BOND = 1413.3419 ANGLE = 3744.8722 DIHED = 5423.1468 VDWAALS = -3951.3303 EEL = -35108.2378 EGB = -7595.4451 1-4 VDW = 1772.7318 1-4 EEL = 23339.6923 RESTRAINT = 0.0000 ESURF = 178.2088 minimization completed, ENE= -.10783019E+05 RMS= 0.172451E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0691E+04 1.7420E+01 1.3067E+02 CD 1420 BOND = 1395.1752 ANGLE = 3757.9274 DIHED = 5458.2008 VDWAALS = -3927.9156 EEL = -35284.7654 EGB = -7477.4059 1-4 VDW = 1840.3690 1-4 EEL = 23369.9716 RESTRAINT = 0.0000 ESURF = 177.6516 minimization completed, ENE= -.10690791E+05 RMS= 0.174198E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0728E+04 1.7218E+01 1.0335E+02 C 6834 BOND = 1411.5894 ANGLE = 3828.0614 DIHED = 5393.1948 VDWAALS = -3978.6601 EEL = -35187.5205 EGB = -7517.2919 1-4 VDW = 1826.7430 1-4 EEL = 23315.8938 RESTRAINT = 0.0000 ESURF = 179.6442 minimization completed, ENE= -.10728346E+05 RMS= 0.172184E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0806E+04 1.7191E+01 1.1746E+02 C 3157 BOND = 1411.3223 ANGLE = 3734.2538 DIHED = 5401.8221 VDWAALS = -3934.4465 EEL = -35095.6806 EGB = -7582.0222 1-4 VDW = 1795.3528 1-4 EEL = 23282.9459 RESTRAINT = 0.0000 ESURF = 180.2236 minimization completed, ENE= -.10806229E+05 RMS= 0.171910E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0737E+04 1.7388E+01 1.1835E+02 CZ 3420 BOND = 1405.7874 ANGLE = 3809.9037 DIHED = 5418.6415 VDWAALS = -3939.3328 EEL = -35112.5356 EGB = -7583.7379 1-4 VDW = 1788.1545 1-4 EEL = 23295.5563 RESTRAINT = 0.0000 ESURF = 180.1620 minimization completed, ENE= -.10737401E+05 RMS= 0.173882E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0771E+04 1.7450E+01 1.2280E+02 C 6077 BOND = 1408.5181 ANGLE = 3713.9236 DIHED = 5399.7514 VDWAALS = -3945.6778 EEL = -35207.0962 EGB = -7561.2447 1-4 VDW = 1831.3186 1-4 EEL = 23410.2311 RESTRAINT = 0.0000 ESURF = 179.7002 minimization completed, ENE= -.10770576E+05 RMS= 0.174496E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0702E+04 1.7362E+01 1.2081E+02 CD 3539 BOND = 1442.8312 ANGLE = 3720.3653 DIHED = 5456.7064 VDWAALS = -3952.3946 EEL = -35142.9451 EGB = -7537.6536 1-4 VDW = 1801.6419 1-4 EEL = 23331.1759 RESTRAINT = 0.0000 ESURF = 178.2700 minimization completed, ENE= -.10702003E+05 RMS= 0.173623E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0791E+04 1.7454E+01 1.1018E+02 CA 5987 BOND = 1457.2785 ANGLE = 3733.8980 DIHED = 5392.1341 VDWAALS = -3927.1327 EEL = -35163.3894 EGB = -7540.0967 1-4 VDW = 1784.6822 1-4 EEL = 23291.7877 RESTRAINT = 0.0000 ESURF = 179.8500 minimization completed, ENE= -.10790988E+05 RMS= 0.174543E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0721E+04 1.7532E+01 1.2289E+02 CD 7727 BOND = 1406.8367 ANGLE = 3783.3056 DIHED = 5427.5323 VDWAALS = -3926.4823 EEL = -35077.3099 EGB = -7576.6123 1-4 VDW = 1759.1717 1-4 EEL = 23303.3200 RESTRAINT = 0.0000 ESURF = 179.6978 minimization completed, ENE= -.10720540E+05 RMS= 0.175322E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0568E+04 1.7669E+01 1.0977E+02 C 1141 BOND = 1407.4434 ANGLE = 3898.6491 DIHED = 5431.6140 VDWAALS = -3907.4449 EEL = -35157.4938 EGB = -7542.6828 1-4 VDW = 1794.9653 1-4 EEL = 23325.2972 RESTRAINT = 0.0000 ESURF = 181.8021 minimization completed, ENE= -.10567850E+05 RMS= 0.176688E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0758E+04 1.7337E+01 1.1053E+02 CD2 5381 BOND = 1399.9193 ANGLE = 3837.5756 DIHED = 5418.4797 VDWAALS = -3928.0736 EEL = -35224.6754 EGB = -7499.6943 1-4 VDW = 1791.7821 1-4 EEL = 23265.1153 RESTRAINT = 0.0000 ESURF = 181.9434 minimization completed, ENE= -.10757628E+05 RMS= 0.173370E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0743E+04 1.7217E+01 1.2078E+02 CG 2960 BOND = 1372.5208 ANGLE = 3766.7320 DIHED = 5434.2243 VDWAALS = -3951.4849 EEL = -35102.0024 EGB = -7499.4531 1-4 VDW = 1808.5327 1-4 EEL = 23246.8887 RESTRAINT = 0.0000 ESURF = 181.5365 minimization completed, ENE= -.10742505E+05 RMS= 0.172169E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0729E+04 1.7601E+01 1.2195E+02 CZ 862 BOND = 1484.0035 ANGLE = 3783.6306 DIHED = 5414.3566 VDWAALS = -3959.5203 EEL = -35267.0471 EGB = -7398.5078 1-4 VDW = 1777.2961 1-4 EEL = 23254.0928 RESTRAINT = 0.0000 ESURF = 182.3188 minimization completed, ENE= -.10729377E+05 RMS= 0.176009E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0768E+04 1.7597E+01 1.1647E+02 C 6379 BOND = 1416.0207 ANGLE = 3802.6874 DIHED = 5392.9246 VDWAALS = -3931.4614 EEL = -35172.7991 EGB = -7521.9649 1-4 VDW = 1789.9816 1-4 EEL = 23275.6792 RESTRAINT = 0.0000 ESURF = 180.8245 minimization completed, ENE= -.10768107E+05 RMS= 0.175969E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0806E+04 1.7080E+01 1.0410E+02 N 6558 BOND = 1378.1798 ANGLE = 3694.6073 DIHED = 5426.1667 VDWAALS = -3951.6898 EEL = -35194.3601 EGB = -7477.6568 1-4 VDW = 1818.0652 1-4 EEL = 23319.8758 RESTRAINT = 0.0000 ESURF = 181.0387 minimization completed, ENE= -.10805773E+05 RMS= 0.170798E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0785E+04 1.7395E+01 1.0778E+02 C 2477 BOND = 1416.7624 ANGLE = 3659.9336 DIHED = 5464.2970 VDWAALS = -3911.9241 EEL = -35274.5153 EGB = -7481.2292 1-4 VDW = 1807.7605 1-4 EEL = 23354.2055 RESTRAINT = 0.0000 ESURF = 179.8662 minimization completed, ENE= -.10784843E+05 RMS= 0.173954E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0676E+04 1.7304E+01 1.1214E+02 CA 5511 BOND = 1393.8718 ANGLE = 3818.4600 DIHED = 5468.0842 VDWAALS = -3934.6159 EEL = -35198.8713 EGB = -7472.6492 1-4 VDW = 1805.2395 1-4 EEL = 23266.4952 RESTRAINT = 0.0000 ESURF = 178.1896 minimization completed, ENE= -.10675796E+05 RMS= 0.173038E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0731E+04 1.7393E+01 1.1802E+02 CG 7071 BOND = 1413.6228 ANGLE = 3773.4721 DIHED = 5409.4021 VDWAALS = -3945.8720 EEL = -35270.5978 EGB = -7387.0827 1-4 VDW = 1822.7549 1-4 EEL = 23273.9632 RESTRAINT = 0.0000 ESURF = 178.9747 minimization completed, ENE= -.10731363E+05 RMS= 0.173925E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0687E+04 1.7442E+01 1.2738E+02 CZ 4241 BOND = 1409.0302 ANGLE = 3800.3128 DIHED = 5436.7554 VDWAALS = -3923.4021 EEL = -35360.8949 EGB = -7335.6733 1-4 VDW = 1818.4717 1-4 EEL = 23288.5018 RESTRAINT = 0.0000 ESURF = 180.2356 minimization completed, ENE= -.10686663E+05 RMS= 0.174423E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0726E+04 1.7342E+01 1.3210E+02 C 134 BOND = 1413.4076 ANGLE = 3738.0973 DIHED = 5435.2654 VDWAALS = -3961.7234 EEL = -35295.2382 EGB = -7404.7008 1-4 VDW = 1839.1056 1-4 EEL = 23328.9139 RESTRAINT = 0.0000 ESURF = 180.8685 minimization completed, ENE= -.10726004E+05 RMS= 0.173424E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0789E+04 1.7097E+01 1.2440E+02 CA 7672 BOND = 1409.7544 ANGLE = 3731.6442 DIHED = 5419.0958 VDWAALS = -3951.1752 EEL = -35116.2692 EGB = -7488.5654 1-4 VDW = 1800.4041 1-4 EEL = 23228.9411 RESTRAINT = 0.0000 ESURF = 177.6053 minimization completed, ENE= -.10788565E+05 RMS= 0.170973E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0783E+04 1.7229E+01 1.1607E+02 C4 7871 BOND = 1378.0288 ANGLE = 3767.8557 DIHED = 5406.1767 VDWAALS = -3956.4981 EEL = -35188.6639 EGB = -7478.9101 1-4 VDW = 1795.5669 1-4 EEL = 23315.9656 RESTRAINT = 0.0000 ESURF = 177.8096 minimization completed, ENE= -.10782669E+05 RMS= 0.172291E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0757E+04 1.7410E+01 1.4832E+02 C 2096 BOND = 1424.5063 ANGLE = 3776.2082 DIHED = 5473.0849 VDWAALS = -3978.3741 EEL = -35220.2402 EGB = -7432.9485 1-4 VDW = 1784.8350 1-4 EEL = 23237.9907 RESTRAINT = 0.0000 ESURF = 177.4543 minimization completed, ENE= -.10757483E+05 RMS= 0.174097E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0781E+04 1.7603E+01 1.1924E+02 CD 3169 BOND = 1476.5501 ANGLE = 3752.2311 DIHED = 5392.7694 VDWAALS = -3932.6524 EEL = -35237.4474 EGB = -7447.0998 1-4 VDW = 1782.5462 1-4 EEL = 23254.7669 RESTRAINT = 0.0000 ESURF = 177.5604 minimization completed, ENE= -.10780775E+05 RMS= 0.176028E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 710.00 ( 7.70% of Gen B) | Calc gb diag 5500.02 (59.63% of Gen B) | Calc gb off-diag 3012.90 (32.67% of Gen B) | Gen Born time 9222.92 (100.0% of Nonbo) | Nonbond force 9222.92 (100.0% of Force) | Bond/Angle/Dihedral 6.86 ( 0.07% of Force) | Force time 9229.79 (100.0% of Runmd) | Runmd Time 9229.79 (99.16% of Total) | Other 77.33 ( 0.83% of Total) | Total time 9307.53 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 19:12:37.039 on 10/19/2010 | Setup done at 19:12:39.565 on 10/19/2010 | Run done at 21:47:44.573 on 10/19/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/19/2010 at 19:12:39 [-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 -1.0787E+04 1.7334E+01 1.0968E+02 C 7436 BOND = 1442.8657 ANGLE = 3773.7563 DIHED = 5435.6070 VDWAALS = -3922.7458 EEL = -35078.8991 EGB = -7617.1789 1-4 VDW = 1742.3325 1-4 EEL = 23256.1663 RESTRAINT = 0.0000 ESURF = 180.6490 minimization completed, ENE= -.10787447E+05 RMS= 0.173345E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0731E+04 1.7344E+01 1.1404E+02 C 5059 BOND = 1404.5431 ANGLE = 3747.7818 DIHED = 5376.8596 VDWAALS = -3948.7940 EEL = -35046.0113 EGB = -7646.7439 1-4 VDW = 1816.2657 1-4 EEL = 23385.1264 RESTRAINT = 0.0000 ESURF = 179.7251 minimization completed, ENE= -.10731248E+05 RMS= 0.173445E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0806E+04 1.7171E+01 1.2609E+02 N 280 BOND = 1391.6582 ANGLE = 3691.0529 DIHED = 5443.1429 VDWAALS = -3960.6967 EEL = -35011.3129 EGB = -7618.5197 1-4 VDW = 1814.5341 1-4 EEL = 23266.1024 RESTRAINT = 0.0000 ESURF = 178.3976 minimization completed, ENE= -.10805641E+05 RMS= 0.171709E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0804E+04 1.7357E+01 1.2995E+02 CZ 6437 BOND = 1426.2776 ANGLE = 3664.2410 DIHED = 5431.8289 VDWAALS = -3926.0516 EEL = -34987.0243 EGB = -7659.7199 1-4 VDW = 1803.1547 1-4 EEL = 23261.1178 RESTRAINT = 0.0000 ESURF = 182.6677 minimization completed, ENE= -.10803508E+05 RMS= 0.173567E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0754E+04 1.7360E+01 1.0770E+02 C 4161 BOND = 1402.8876 ANGLE = 3718.5393 DIHED = 5437.8278 VDWAALS = -3945.5761 EEL = -35068.3305 EGB = -7576.7519 1-4 VDW = 1801.3327 1-4 EEL = 23295.6193 RESTRAINT = 0.0000 ESURF = 180.0041 minimization completed, ENE= -.10754448E+05 RMS= 0.173603E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0824E+04 1.7309E+01 1.0919E+02 C 5622 BOND = 1427.4950 ANGLE = 3776.0297 DIHED = 5417.1608 VDWAALS = -3952.0105 EEL = -34980.5125 EGB = -7704.1825 1-4 VDW = 1794.8695 1-4 EEL = 23216.2836 RESTRAINT = 0.0000 ESURF = 180.7399 minimization completed, ENE= -.10824127E+05 RMS= 0.173094E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0789E+04 1.7179E+01 9.8842E+01 C 3403 BOND = 1377.8248 ANGLE = 3723.3745 DIHED = 5437.1765 VDWAALS = -3911.0354 EEL = -35145.5890 EGB = -7447.8205 1-4 VDW = 1813.2855 1-4 EEL = 23184.9787 RESTRAINT = 0.0000 ESURF = 179.0475 minimization completed, ENE= -.10788758E+05 RMS= 0.171788E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0719E+04 1.7221E+01 1.0685E+02 C 3639 BOND = 1448.5797 ANGLE = 3748.9244 DIHED = 5423.5879 VDWAALS = -3894.5854 EEL = -35263.4780 EGB = -7416.5817 1-4 VDW = 1790.8536 1-4 EEL = 23264.2075 RESTRAINT = 0.0000 ESURF = 179.7525 minimization completed, ENE= -.10718739E+05 RMS= 0.172211E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0754E+04 1.7461E+01 1.0724E+02 CG 7259 BOND = 1424.1438 ANGLE = 3753.8689 DIHED = 5432.9458 VDWAALS = -3888.9183 EEL = -35273.8151 EGB = -7452.3326 1-4 VDW = 1774.4583 1-4 EEL = 23293.8667 RESTRAINT = 0.0000 ESURF = 181.9438 minimization completed, ENE= -.10753839E+05 RMS= 0.174608E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0782E+04 1.7131E+01 1.1195E+02 C 7687 BOND = 1395.4711 ANGLE = 3715.2007 DIHED = 5402.8449 VDWAALS = -3919.7815 EEL = -35189.8986 EGB = -7408.0213 1-4 VDW = 1809.7651 1-4 EEL = 23230.0249 RESTRAINT = 0.0000 ESURF = 182.0896 minimization completed, ENE= -.10782305E+05 RMS= 0.171305E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0723E+04 1.7512E+01 1.1568E+02 C 2907 BOND = 1468.3085 ANGLE = 3688.9384 DIHED = 5450.6044 VDWAALS = -3877.4674 EEL = -35386.0809 EGB = -7360.1730 1-4 VDW = 1824.6333 1-4 EEL = 23287.5479 RESTRAINT = 0.0000 ESURF = 180.7545 minimization completed, ENE= -.10722934E+05 RMS= 0.175125E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0732E+04 1.7168E+01 1.1235E+02 CD 4522 BOND = 1386.9525 ANGLE = 3807.6583 DIHED = 5462.2414 VDWAALS = -3937.6153 EEL = -35147.4782 EGB = -7539.8396 1-4 VDW = 1813.1120 1-4 EEL = 23241.3860 RESTRAINT = 0.0000 ESURF = 181.1605 minimization completed, ENE= -.10732422E+05 RMS= 0.171679E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0773E+04 1.7310E+01 9.8730E+01 C 1812 BOND = 1432.6779 ANGLE = 3662.2037 DIHED = 5497.9364 VDWAALS = -3876.5460 EEL = -35278.9894 EGB = -7457.9213 1-4 VDW = 1794.5729 1-4 EEL = 23272.3462 RESTRAINT = 0.0000 ESURF = 181.0707 minimization completed, ENE= -.10772649E+05 RMS= 0.173095E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0781E+04 1.7265E+01 1.1739E+02 C 3384 BOND = 1389.0471 ANGLE = 3703.7718 DIHED = 5395.2596 VDWAALS = -3872.3068 EEL = -35303.5610 EGB = -7453.9967 1-4 VDW = 1826.7100 1-4 EEL = 23353.2378 RESTRAINT = 0.0000 ESURF = 181.2058 minimization completed, ENE= -.10780632E+05 RMS= 0.172652E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0702E+04 1.7409E+01 1.2805E+02 C 5434 BOND = 1424.5028 ANGLE = 3776.6524 DIHED = 5430.1964 VDWAALS = -3953.3325 EEL = -35050.6431 EGB = -7557.4918 1-4 VDW = 1785.1796 1-4 EEL = 23263.0277 RESTRAINT = 0.0000 ESURF = 180.2859 minimization completed, ENE= -.10701623E+05 RMS= 0.174087E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0662E+04 1.7548E+01 1.1062E+02 C 4108 BOND = 1462.1713 ANGLE = 3794.5198 DIHED = 5450.2025 VDWAALS = -3865.0990 EEL = -35297.3532 EGB = -7462.1154 1-4 VDW = 1765.6156 1-4 EEL = 23306.7879 RESTRAINT = 0.0000 ESURF = 183.2600 minimization completed, ENE= -.10662011E+05 RMS= 0.175480E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0708E+04 1.7569E+01 1.1718E+02 CZ 4241 BOND = 1459.4357 ANGLE = 3782.1979 DIHED = 5416.4793 VDWAALS = -3921.8924 EEL = -35291.4515 EGB = -7436.7530 1-4 VDW = 1788.0250 1-4 EEL = 23315.1169 RESTRAINT = 0.0000 ESURF = 181.1039 minimization completed, ENE= -.10707738E+05 RMS= 0.175687E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0731E+04 1.7226E+01 9.6652E+01 C 4421 BOND = 1454.6315 ANGLE = 3776.3328 DIHED = 5419.6659 VDWAALS = -3921.1348 EEL = -35109.4743 EGB = -7558.4254 1-4 VDW = 1779.5962 1-4 EEL = 23247.4415 RESTRAINT = 0.0000 ESURF = 180.0934 minimization completed, ENE= -.10731273E+05 RMS= 0.172258E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0799E+04 1.7272E+01 1.1610E+02 CG 102 BOND = 1430.5229 ANGLE = 3712.8519 DIHED = 5429.6244 VDWAALS = -3951.0132 EEL = -35124.0748 EGB = -7524.8152 1-4 VDW = 1791.8849 1-4 EEL = 23255.9184 RESTRAINT = 0.0000 ESURF = 179.8888 minimization completed, ENE= -.10799212E+05 RMS= 0.172719E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0738E+04 1.7114E+01 1.0114E+02 CB 3788 BOND = 1381.7136 ANGLE = 3805.9120 DIHED = 5397.0397 VDWAALS = -3906.2474 EEL = -34887.8612 EGB = -7740.7249 1-4 VDW = 1786.8818 1-4 EEL = 23246.2015 RESTRAINT = 0.0000 ESURF = 179.4747 minimization completed, ENE= -.10737610E+05 RMS= 0.171141E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0571E+04 1.7614E+01 1.4377E+02 C 2689 BOND = 1476.5454 ANGLE = 3816.6406 DIHED = 5471.0014 VDWAALS = -3925.2771 EEL = -35027.2686 EGB = -7660.1584 1-4 VDW = 1817.4650 1-4 EEL = 23280.7483 RESTRAINT = 0.0000 ESURF = 179.3776 minimization completed, ENE= -.10570926E+05 RMS= 0.176135E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0702E+04 1.7257E+01 1.1234E+02 C 573 BOND = 1441.2684 ANGLE = 3829.8912 DIHED = 5441.0371 VDWAALS = -3920.9520 EEL = -35149.4820 EGB = -7486.5191 1-4 VDW = 1776.7508 1-4 EEL = 23185.3747 RESTRAINT = 0.0000 ESURF = 181.0019 minimization completed, ENE= -.10701629E+05 RMS= 0.172571E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0741E+04 1.7132E+01 1.2509E+02 N 4651 BOND = 1405.6844 ANGLE = 3800.3918 DIHED = 5426.0716 VDWAALS = -3909.0806 EEL = -35269.3890 EGB = -7474.3059 1-4 VDW = 1785.7219 1-4 EEL = 23312.5935 RESTRAINT = 0.0000 ESURF = 180.8608 minimization completed, ENE= -.10741452E+05 RMS= 0.171323E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0679E+04 1.7406E+01 1.1465E+02 C 7668 BOND = 1401.7184 ANGLE = 3761.4233 DIHED = 5425.0010 VDWAALS = -3893.5574 EEL = -35078.6575 EGB = -7599.9974 1-4 VDW = 1809.0578 1-4 EEL = 23316.6252 RESTRAINT = 0.0000 ESURF = 179.8321 minimization completed, ENE= -.10678555E+05 RMS= 0.174057E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0682E+04 1.7565E+01 1.0981E+02 C 2086 BOND = 1456.5587 ANGLE = 3759.2210 DIHED = 5428.3042 VDWAALS = -3979.9378 EEL = -35010.1097 EGB = -7587.0869 1-4 VDW = 1789.8616 1-4 EEL = 23282.6572 RESTRAINT = 0.0000 ESURF = 179.0159 minimization completed, ENE= -.10681516E+05 RMS= 0.175649E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0655E+04 1.7308E+01 1.1539E+02 C 43 BOND = 1414.2471 ANGLE = 3749.9237 DIHED = 5411.9389 VDWAALS = -3938.1658 EEL = -35020.7162 EGB = -7613.1836 1-4 VDW = 1797.8439 1-4 EEL = 23363.2032 RESTRAINT = 0.0000 ESURF = 180.1265 minimization completed, ENE= -.10654782E+05 RMS= 0.173084E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0645E+04 1.7690E+01 1.1263E+02 C 382 BOND = 1444.5023 ANGLE = 3776.9777 DIHED = 5394.8654 VDWAALS = -3898.3221 EEL = -35173.2513 EGB = -7576.6681 1-4 VDW = 1836.7203 1-4 EEL = 23370.0622 RESTRAINT = 0.0000 ESURF = 180.1927 minimization completed, ENE= -.10644921E+05 RMS= 0.176899E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0700E+04 1.7387E+01 1.2332E+02 C 4092 BOND = 1396.1712 ANGLE = 3781.2014 DIHED = 5429.7057 VDWAALS = -3963.1153 EEL = -35031.0090 EGB = -7639.2890 1-4 VDW = 1808.1746 1-4 EEL = 23337.6266 RESTRAINT = 0.0000 ESURF = 180.8277 minimization completed, ENE= -.10699706E+05 RMS= 0.173867E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0780E+04 1.7448E+01 1.2659E+02 C 156 BOND = 1423.4798 ANGLE = 3718.2344 DIHED = 5412.1062 VDWAALS = -3917.1478 EEL = -35312.0624 EGB = -7440.0662 1-4 VDW = 1801.0150 1-4 EEL = 23357.9895 RESTRAINT = 0.0000 ESURF = 176.4889 minimization completed, ENE= -.10779963E+05 RMS= 0.174476E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0735E+04 1.7581E+01 1.1221E+02 C 4935 BOND = 1427.4131 ANGLE = 3797.1121 DIHED = 5411.7367 VDWAALS = -3903.1572 EEL = -35348.0291 EGB = -7401.4837 1-4 VDW = 1795.1383 1-4 EEL = 23305.3168 RESTRAINT = 0.0000 ESURF = 180.8315 minimization completed, ENE= -.10735121E+05 RMS= 0.175809E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0702E+04 1.7678E+01 1.2634E+02 C 819 BOND = 1474.8867 ANGLE = 3729.5268 DIHED = 5367.8751 VDWAALS = -3938.6276 EEL = -35191.0185 EGB = -7502.1282 1-4 VDW = 1815.7397 1-4 EEL = 23363.3432 RESTRAINT = 0.0000 ESURF = 178.4053 minimization completed, ENE= -.10701998E+05 RMS= 0.176777E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0735E+04 1.7337E+01 1.1841E+02 C 7144 BOND = 1371.2730 ANGLE = 3795.2901 DIHED = 5411.2687 VDWAALS = -3963.4880 EEL = -35162.3974 EGB = -7566.6574 1-4 VDW = 1842.2861 1-4 EEL = 23358.3716 RESTRAINT = 0.0000 ESURF = 178.8327 minimization completed, ENE= -.10735220E+05 RMS= 0.173373E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0839E+04 1.7318E+01 1.2144E+02 C 7074 BOND = 1377.3538 ANGLE = 3732.2903 DIHED = 5375.5805 VDWAALS = -3925.1128 EEL = -34950.6653 EGB = -7744.5510 1-4 VDW = 1800.7370 1-4 EEL = 23316.7360 RESTRAINT = 0.0000 ESURF = 179.1196 minimization completed, ENE= -.10838512E+05 RMS= 0.173179E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0739E+04 1.7258E+01 1.2953E+02 CG 3379 BOND = 1423.8395 ANGLE = 3680.0468 DIHED = 5444.1376 VDWAALS = -3975.9192 EEL = -34965.4545 EGB = -7605.8186 1-4 VDW = 1795.8028 1-4 EEL = 23285.8401 RESTRAINT = 0.0000 ESURF = 178.4074 minimization completed, ENE= -.10739118E+05 RMS= 0.172576E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0711E+04 1.7238E+01 1.1948E+02 NE 171 BOND = 1411.9487 ANGLE = 3810.8605 DIHED = 5408.0169 VDWAALS = -4033.3660 EEL = -35003.8036 EGB = -7576.2495 1-4 VDW = 1806.8883 1-4 EEL = 23288.3634 RESTRAINT = 0.0000 ESURF = 176.6938 minimization completed, ENE= -.10710648E+05 RMS= 0.172377E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0713E+04 1.7420E+01 1.1718E+02 CA 2605 BOND = 1385.2842 ANGLE = 3726.6867 DIHED = 5411.8087 VDWAALS = -3994.1394 EEL = -34968.4402 EGB = -7568.7743 1-4 VDW = 1820.0572 1-4 EEL = 23295.9399 RESTRAINT = 0.0000 ESURF = 178.4063 minimization completed, ENE= -.10713171E+05 RMS= 0.174200E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0643E+04 1.7488E+01 1.0437E+02 C 1141 BOND = 1423.0953 ANGLE = 3791.8548 DIHED = 5447.8711 VDWAALS = -3901.1282 EEL = -35055.0721 EGB = -7631.5282 1-4 VDW = 1820.9181 1-4 EEL = 23282.2620 RESTRAINT = 0.0000 ESURF = 178.9031 minimization completed, ENE= -.10642824E+05 RMS= 0.174884E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0766E+04 1.7103E+01 1.0241E+02 CD 3539 BOND = 1402.6251 ANGLE = 3739.4883 DIHED = 5456.1919 VDWAALS = -3939.6940 EEL = -35002.4631 EGB = -7643.4151 1-4 VDW = 1781.3051 1-4 EEL = 23259.4670 RESTRAINT = 0.0000 ESURF = 180.2031 minimization completed, ENE= -.10766292E+05 RMS= 0.171031E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0800E+04 1.7240E+01 1.2728E+02 CG 2253 BOND = 1404.3805 ANGLE = 3742.2507 DIHED = 5425.8402 VDWAALS = -3958.5125 EEL = -34996.5372 EGB = -7646.9259 1-4 VDW = 1791.2407 1-4 EEL = 23260.8751 RESTRAINT = 0.0000 ESURF = 177.6010 minimization completed, ENE= -.10799788E+05 RMS= 0.172400E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0654E+04 1.7283E+01 1.1515E+02 C 301 BOND = 1410.0391 ANGLE = 3752.7363 DIHED = 5403.8564 VDWAALS = -3923.9660 EEL = -35149.0510 EGB = -7495.2748 1-4 VDW = 1806.0357 1-4 EEL = 23358.6523 RESTRAINT = 0.0000 ESURF = 182.5621 minimization completed, ENE= -.10654410E+05 RMS= 0.172828E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0748E+04 1.7374E+01 1.1128E+02 CD 5056 BOND = 1437.4774 ANGLE = 3744.0812 DIHED = 5419.9646 VDWAALS = -3937.1459 EEL = -35182.9378 EGB = -7536.4124 1-4 VDW = 1787.5272 1-4 EEL = 23337.8137 RESTRAINT = 0.0000 ESURF = 181.5131 minimization completed, ENE= -.10748119E+05 RMS= 0.173738E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0785E+04 1.7547E+01 1.3213E+02 PG 7838 BOND = 1433.3196 ANGLE = 3754.8430 DIHED = 5400.8548 VDWAALS = -3909.4105 EEL = -35266.4736 EGB = -7421.1915 1-4 VDW = 1793.7115 1-4 EEL = 23248.4043 RESTRAINT = 0.0000 ESURF = 181.4087 minimization completed, ENE= -.10784534E+05 RMS= 0.175472E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0803E+04 1.7302E+01 1.2046E+02 CD 5041 BOND = 1408.6121 ANGLE = 3723.7474 DIHED = 5434.1604 VDWAALS = -3884.1165 EEL = -35352.1293 EGB = -7353.7021 1-4 VDW = 1800.4391 1-4 EEL = 23238.8081 RESTRAINT = 0.0000 ESURF = 180.8168 minimization completed, ENE= -.10803364E+05 RMS= 0.173016E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0797E+04 1.7122E+01 1.1392E+02 CD 2137 BOND = 1334.0212 ANGLE = 3763.3975 DIHED = 5397.6185 VDWAALS = -3904.8040 EEL = -35369.8741 EGB = -7412.6286 1-4 VDW = 1837.7703 1-4 EEL = 23375.9225 RESTRAINT = 0.0000 ESURF = 181.2019 minimization completed, ENE= -.10797375E+05 RMS= 0.171222E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0830E+04 1.7195E+01 1.1874E+02 C 4551 BOND = 1359.9590 ANGLE = 3716.8411 DIHED = 5415.4383 VDWAALS = -3904.7247 EEL = -35374.3533 EGB = -7443.1455 1-4 VDW = 1824.3511 1-4 EEL = 23395.2879 RESTRAINT = 0.0000 ESURF = 179.9386 minimization completed, ENE= -.10830407E+05 RMS= 0.171952E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0823E+04 1.7253E+01 1.2248E+02 C 5793 BOND = 1367.3380 ANGLE = 3723.8820 DIHED = 5371.6030 VDWAALS = -3935.3192 EEL = -35132.0862 EGB = -7508.5261 1-4 VDW = 1824.3118 1-4 EEL = 23285.8078 RESTRAINT = 0.0000 ESURF = 180.2995 minimization completed, ENE= -.10822689E+05 RMS= 0.172531E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0678E+04 1.7596E+01 1.2649E+02 C 5777 BOND = 1494.6496 ANGLE = 3750.8004 DIHED = 5432.0179 VDWAALS = -3961.2369 EEL = -35192.7258 EGB = -7495.0513 1-4 VDW = 1777.8726 1-4 EEL = 23336.1941 RESTRAINT = 0.0000 ESURF = 179.3303 minimization completed, ENE= -.10678149E+05 RMS= 0.175960E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0794E+04 1.7395E+01 1.4005E+02 C 653 BOND = 1430.2017 ANGLE = 3724.6221 DIHED = 5410.2302 VDWAALS = -3967.3823 EEL = -35183.5766 EGB = -7389.1610 1-4 VDW = 1767.0603 1-4 EEL = 23234.3238 RESTRAINT = 0.0000 ESURF = 179.8704 minimization completed, ENE= -.10793811E+05 RMS= 0.173953E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0785E+04 1.7214E+01 1.1041E+02 C 7730 BOND = 1357.5330 ANGLE = 3791.4230 DIHED = 5428.9888 VDWAALS = -3946.1733 EEL = -35240.2093 EGB = -7487.2892 1-4 VDW = 1801.0040 1-4 EEL = 23329.5661 RESTRAINT = 0.0000 ESURF = 180.1788 minimization completed, ENE= -.10784978E+05 RMS= 0.172135E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0828E+04 1.7229E+01 1.1771E+02 C 134 BOND = 1407.8546 ANGLE = 3669.8449 DIHED = 5438.3307 VDWAALS = -3952.1415 EEL = -35342.5758 EGB = -7370.9081 1-4 VDW = 1791.3595 1-4 EEL = 23350.7868 RESTRAINT = 0.0000 ESURF = 179.1756 minimization completed, ENE= -.10828273E+05 RMS= 0.172286E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 705.41 ( 7.64% of Gen B) | Calc gb diag 5495.20 (59.52% of Gen B) | Calc gb off-diag 3031.71 (32.84% of Gen B) | Gen Born time 9232.33 (100.0% of Nonbo) | Nonbond force 9232.33 (99.89% of Force) | Bond/Angle/Dihedral 9.86 ( 0.11% of Force) | Force time 9242.20 (100.0% of Runmd) | Runmd Time 9242.20 (99.00% of Total) | Other 93.27 ( 1.00% of Total) | Total time 9335.89 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 19:12:37.031 on 10/19/2010 | Setup done at 19:12:40.797 on 10/19/2010 | Run done at 21:48:12.924 on 10/19/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/19/2010 at 19:12:38 [-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 -1.0725E+04 1.7588E+01 1.2433E+02 C 1742 BOND = 1470.9544 ANGLE = 3716.8393 DIHED = 5374.0045 VDWAALS = -3927.7414 EEL = -35219.8701 EGB = -7425.6118 1-4 VDW = 1823.7408 1-4 EEL = 23284.5634 RESTRAINT = 0.0000 ESURF = 177.7735 minimization completed, ENE= -.10725347E+05 RMS= 0.175875E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0753E+04 1.7405E+01 1.1228E+02 CZ 1000 BOND = 1387.5963 ANGLE = 3773.7802 DIHED = 5426.4967 VDWAALS = -3945.5848 EEL = -35160.1950 EGB = -7509.3996 1-4 VDW = 1799.2448 1-4 EEL = 23296.4768 RESTRAINT = 0.0000 ESURF = 178.8277 minimization completed, ENE= -.10752757E+05 RMS= 0.174051E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0749E+04 1.7092E+01 9.6488E+01 CD 4694 BOND = 1362.7463 ANGLE = 3774.1991 DIHED = 5415.6644 VDWAALS = -3920.4625 EEL = -35065.2841 EGB = -7678.8928 1-4 VDW = 1812.4912 1-4 EEL = 23370.7016 RESTRAINT = 0.0000 ESURF = 179.3564 minimization completed, ENE= -.10749480E+05 RMS= 0.170924E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0869E+04 1.7185E+01 1.1604E+02 CG 995 BOND = 1382.3305 ANGLE = 3808.0258 DIHED = 5398.0202 VDWAALS = -3942.4041 EEL = -35140.3308 EGB = -7551.4543 1-4 VDW = 1766.5006 1-4 EEL = 23231.2764 RESTRAINT = 0.0000 ESURF = 179.0375 minimization completed, ENE= -.10868998E+05 RMS= 0.171850E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0842E+04 1.7304E+01 1.1887E+02 CD 5968 BOND = 1389.0720 ANGLE = 3714.8949 DIHED = 5397.3447 VDWAALS = -3925.5870 EEL = -35269.2840 EGB = -7464.4912 1-4 VDW = 1814.9640 1-4 EEL = 23321.8161 RESTRAINT = 0.0000 ESURF = 178.8980 minimization completed, ENE= -.10842372E+05 RMS= 0.173036E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0707E+04 1.7409E+01 1.2291E+02 C 5395 BOND = 1403.9329 ANGLE = 3777.8217 DIHED = 5397.2309 VDWAALS = -3902.3465 EEL = -35354.6344 EGB = -7391.8129 1-4 VDW = 1822.5076 1-4 EEL = 23361.3475 RESTRAINT = 0.0000 ESURF = 178.8704 minimization completed, ENE= -.10707083E+05 RMS= 0.174088E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0649E+04 1.7689E+01 1.3330E+02 CG 782 BOND = 1453.8862 ANGLE = 3829.0809 DIHED = 5418.5151 VDWAALS = -3935.9963 EEL = -35201.9493 EGB = -7420.1732 1-4 VDW = 1799.7484 1-4 EEL = 23231.1140 RESTRAINT = 0.0000 ESURF = 177.2102 minimization completed, ENE= -.10648564E+05 RMS= 0.176885E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0705E+04 1.7311E+01 1.0327E+02 CA 5176 BOND = 1389.9220 ANGLE = 3815.3414 DIHED = 5403.6242 VDWAALS = -3935.4652 EEL = -35215.1243 EGB = -7456.2977 1-4 VDW = 1802.8504 1-4 EEL = 23313.9408 RESTRAINT = 0.0000 ESURF = 176.2216 minimization completed, ENE= -.10704987E+05 RMS= 0.173107E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0740E+04 1.7351E+01 1.1376E+02 C 4280 BOND = 1395.2234 ANGLE = 3720.8631 DIHED = 5446.6523 VDWAALS = -3917.1505 EEL = -35153.5186 EGB = -7554.4621 1-4 VDW = 1796.6803 1-4 EEL = 23346.8817 RESTRAINT = 0.0000 ESURF = 178.9337 minimization completed, ENE= -.10739897E+05 RMS= 0.173506E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0713E+04 1.7324E+01 1.2505E+02 CG 3293 BOND = 1448.4555 ANGLE = 3634.0550 DIHED = 5403.3219 VDWAALS = -3928.1473 EEL = -34942.2487 EGB = -7609.5515 1-4 VDW = 1846.8110 1-4 EEL = 23254.4199 RESTRAINT = 0.0000 ESURF = 179.7750 minimization completed, ENE= -.10713109E+05 RMS= 0.173236E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0790E+04 1.6960E+01 1.0035E+02 N 2588 BOND = 1332.4200 ANGLE = 3755.9693 DIHED = 5437.3648 VDWAALS = -3935.3307 EEL = -35125.0751 EGB = -7555.4635 1-4 VDW = 1801.2012 1-4 EEL = 23318.3435 RESTRAINT = 0.0000 ESURF = 180.7859 minimization completed, ENE= -.10789785E+05 RMS= 0.169601E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0786E+04 1.7322E+01 1.0927E+02 N 7180 BOND = 1424.8379 ANGLE = 3745.0334 DIHED = 5411.6259 VDWAALS = -3928.5693 EEL = -35045.5463 EGB = -7604.5800 1-4 VDW = 1798.4717 1-4 EEL = 23232.6014 RESTRAINT = 0.0000 ESURF = 179.7344 minimization completed, ENE= -.10786391E+05 RMS= 0.173217E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0767E+04 1.7338E+01 1.1972E+02 C 986 BOND = 1412.1324 ANGLE = 3745.8372 DIHED = 5388.0736 VDWAALS = -3936.5705 EEL = -34877.8704 EGB = -7730.8215 1-4 VDW = 1804.3958 1-4 EEL = 23247.1589 RESTRAINT = 0.0000 ESURF = 180.7029 minimization completed, ENE= -.10766962E+05 RMS= 0.173381E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0720E+04 1.7427E+01 1.1018E+02 C 5971 BOND = 1434.8472 ANGLE = 3718.5101 DIHED = 5429.8667 VDWAALS = -3932.8503 EEL = -35014.0300 EGB = -7602.3997 1-4 VDW = 1816.1581 1-4 EEL = 23251.7083 RESTRAINT = 0.0000 ESURF = 178.5851 minimization completed, ENE= -.10719605E+05 RMS= 0.174269E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0692E+04 1.7410E+01 1.1381E+02 C 2198 BOND = 1430.5999 ANGLE = 3803.5759 DIHED = 5442.6167 VDWAALS = -3921.0913 EEL = -35250.6309 EGB = -7452.2319 1-4 VDW = 1795.3557 1-4 EEL = 23280.1448 RESTRAINT = 0.0000 ESURF = 179.9621 minimization completed, ENE= -.10691699E+05 RMS= 0.174098E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0729E+04 1.7385E+01 1.4106E+02 C 4617 BOND = 1449.4799 ANGLE = 3801.0280 DIHED = 5411.5148 VDWAALS = -3924.0005 EEL = -35170.9144 EGB = -7546.9469 1-4 VDW = 1801.3052 1-4 EEL = 23267.9333 RESTRAINT = 0.0000 ESURF = 181.8582 minimization completed, ENE= -.10728742E+05 RMS= 0.173854E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0805E+04 1.7297E+01 1.1641E+02 CB 5585 BOND = 1381.9770 ANGLE = 3780.8928 DIHED = 5368.2699 VDWAALS = -3910.2524 EEL = -35235.9979 EGB = -7482.8308 1-4 VDW = 1785.2526 1-4 EEL = 23324.9952 RESTRAINT = 0.0000 ESURF = 182.2421 minimization completed, ENE= -.10805451E+05 RMS= 0.172974E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0649E+04 1.7289E+01 1.1683E+02 C 937 BOND = 1386.1501 ANGLE = 3788.9125 DIHED = 5448.7891 VDWAALS = -3871.6042 EEL = -35029.7250 EGB = -7633.1099 1-4 VDW = 1800.5952 1-4 EEL = 23281.8520 RESTRAINT = 0.0000 ESURF = 179.5705 minimization completed, ENE= -.10648570E+05 RMS= 0.172887E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0747E+04 1.7394E+01 1.1570E+02 C 952 BOND = 1418.6620 ANGLE = 3734.2995 DIHED = 5428.9921 VDWAALS = -3971.1402 EEL = -35107.5879 EGB = -7528.6579 1-4 VDW = 1774.3123 1-4 EEL = 23322.4997 RESTRAINT = 0.0000 ESURF = 181.8230 minimization completed, ENE= -.10746797E+05 RMS= 0.173940E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0626E+04 1.7325E+01 1.4011E+02 C 5748 BOND = 1425.4146 ANGLE = 3783.7758 DIHED = 5405.6736 VDWAALS = -3866.3659 EEL = -34915.5229 EGB = -7691.8692 1-4 VDW = 1779.7830 1-4 EEL = 23270.0264 RESTRAINT = 0.0000 ESURF = 183.5454 minimization completed, ENE= -.10625539E+05 RMS= 0.173251E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0819E+04 1.7461E+01 1.0892E+02 C 1103 BOND = 1429.7806 ANGLE = 3685.8272 DIHED = 5406.9679 VDWAALS = -3927.3343 EEL = -35158.9587 EGB = -7589.9538 1-4 VDW = 1814.0138 1-4 EEL = 23338.9698 RESTRAINT = 0.0000 ESURF = 181.3774 minimization completed, ENE= -.10819310E+05 RMS= 0.174613E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0683E+04 1.7172E+01 1.2103E+02 C 4200 BOND = 1363.7446 ANGLE = 3824.2270 DIHED = 5431.6465 VDWAALS = -3909.6323 EEL = -34929.1940 EGB = -7631.9456 1-4 VDW = 1779.4574 1-4 EEL = 23207.5232 RESTRAINT = 0.0000 ESURF = 181.5518 minimization completed, ENE= -.10682621E+05 RMS= 0.171721E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0842E+04 1.7237E+01 1.0639E+02 C 3011 BOND = 1422.1179 ANGLE = 3704.4839 DIHED = 5424.3692 VDWAALS = -3941.1271 EEL = -34991.5424 EGB = -7675.5041 1-4 VDW = 1783.6624 1-4 EEL = 23249.8062 RESTRAINT = 0.0000 ESURF = 181.6074 minimization completed, ENE= -.10842126E+05 RMS= 0.172370E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0764E+04 1.7493E+01 1.1152E+02 C 589 BOND = 1405.4813 ANGLE = 3682.4276 DIHED = 5460.0066 VDWAALS = -3914.4532 EEL = -35057.1306 EGB = -7663.7876 1-4 VDW = 1803.0573 1-4 EEL = 23335.7499 RESTRAINT = 0.0000 ESURF = 184.2957 minimization completed, ENE= -.10764353E+05 RMS= 0.174932E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0836E+04 1.7134E+01 1.1433E+02 N 3554 BOND = 1321.8439 ANGLE = 3794.4378 DIHED = 5394.1237 VDWAALS = -3918.8845 EEL = -35025.3322 EGB = -7642.7458 1-4 VDW = 1786.6344 1-4 EEL = 23273.5352 RESTRAINT = 0.0000 ESURF = 180.5789 minimization completed, ENE= -.10835809E+05 RMS= 0.171337E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0814E+04 1.7300E+01 1.1357E+02 CG 6862 BOND = 1451.5017 ANGLE = 3632.5678 DIHED = 5457.6670 VDWAALS = -3905.7470 EEL = -34984.9483 EGB = -7650.2666 1-4 VDW = 1784.0905 1-4 EEL = 23218.7833 RESTRAINT = 0.0000 ESURF = 182.3871 minimization completed, ENE= -.10813965E+05 RMS= 0.173004E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0741E+04 1.7226E+01 1.0930E+02 C 5847 BOND = 1405.7025 ANGLE = 3735.6636 DIHED = 5388.2567 VDWAALS = -3947.3940 EEL = -34927.1380 EGB = -7677.2958 1-4 VDW = 1792.9103 1-4 EEL = 23307.2598 RESTRAINT = 0.0000 ESURF = 181.4587 minimization completed, ENE= -.10740576E+05 RMS= 0.172260E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0685E+04 1.7504E+01 1.1452E+02 C 2233 BOND = 1428.8143 ANGLE = 3791.7267 DIHED = 5422.4684 VDWAALS = -3941.8650 EEL = -35107.5238 EGB = -7570.4121 1-4 VDW = 1804.4457 1-4 EEL = 23304.7024 RESTRAINT = 0.0000 ESURF = 182.4000 minimization completed, ENE= -.10685243E+05 RMS= 0.175045E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0834E+04 1.7115E+01 9.9892E+01 C 2005 BOND = 1415.3480 ANGLE = 3701.2590 DIHED = 5383.0531 VDWAALS = -3931.8981 EEL = -35166.5779 EGB = -7551.6672 1-4 VDW = 1801.9149 1-4 EEL = 23332.6974 RESTRAINT = 0.0000 ESURF = 181.7688 minimization completed, ENE= -.10834102E+05 RMS= 0.171149E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0801E+04 1.7312E+01 1.4083E+02 CG 2050 BOND = 1420.3992 ANGLE = 3723.5905 DIHED = 5383.5108 VDWAALS = -3930.9718 EEL = -35130.0489 EGB = -7552.7881 1-4 VDW = 1796.8331 1-4 EEL = 23309.2751 RESTRAINT = 0.0000 ESURF = 179.6033 minimization completed, ENE= -.10800597E+05 RMS= 0.173120E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0807E+04 1.7322E+01 1.3395E+02 CB 5481 BOND = 1439.3492 ANGLE = 3689.8918 DIHED = 5423.2881 VDWAALS = -3983.1864 EEL = -35041.6029 EGB = -7598.5308 1-4 VDW = 1807.3328 1-4 EEL = 23276.2450 RESTRAINT = 0.0000 ESURF = 180.6592 minimization completed, ENE= -.10806554E+05 RMS= 0.173223E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0835E+04 1.7309E+01 1.1362E+02 C 4544 BOND = 1447.1198 ANGLE = 3727.5864 DIHED = 5380.2437 VDWAALS = -3959.8719 EEL = -34887.0594 EGB = -7657.5362 1-4 VDW = 1780.6337 1-4 EEL = 23153.9022 RESTRAINT = 0.0000 ESURF = 179.7837 minimization completed, ENE= -.10835198E+05 RMS= 0.173095E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0741E+04 1.7473E+01 1.3348E+02 C 4602 BOND = 1450.6457 ANGLE = 3701.0322 DIHED = 5439.0231 VDWAALS = -3957.6230 EEL = -35042.1113 EGB = -7573.2365 1-4 VDW = 1811.6671 1-4 EEL = 23249.1963 RESTRAINT = 0.0000 ESURF = 180.8276 minimization completed, ENE= -.10740579E+05 RMS= 0.174726E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0738E+04 1.7171E+01 1.1329E+02 C 5044 BOND = 1395.2980 ANGLE = 3762.1253 DIHED = 5424.6689 VDWAALS = -3970.9070 EEL = -35130.1494 EGB = -7472.2832 1-4 VDW = 1811.5698 1-4 EEL = 23261.0694 RESTRAINT = 0.0000 ESURF = 180.2468 minimization completed, ENE= -.10738361E+05 RMS= 0.171710E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0745E+04 1.7323E+01 1.1409E+02 C 4200 BOND = 1393.9696 ANGLE = 3697.8794 DIHED = 5424.0565 VDWAALS = -3867.9556 EEL = -35183.5231 EGB = -7475.5372 1-4 VDW = 1829.0953 1-4 EEL = 23257.0433 RESTRAINT = 0.0000 ESURF = 180.3619 minimization completed, ENE= -.10744610E+05 RMS= 0.173235E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0681E+04 1.7333E+01 9.8843E+01 C 6444 BOND = 1451.0918 ANGLE = 3856.2315 DIHED = 5378.7734 VDWAALS = -3912.1156 EEL = -35054.8311 EGB = -7631.5087 1-4 VDW = 1792.4231 1-4 EEL = 23256.5524 RESTRAINT = 0.0000 ESURF = 182.6737 minimization completed, ENE= -.10680709E+05 RMS= 0.173327E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0689E+04 1.7467E+01 1.1698E+02 C 2789 BOND = 1440.8139 ANGLE = 3785.1764 DIHED = 5399.0099 VDWAALS = -3857.3457 EEL = -35093.7924 EGB = -7611.1243 1-4 VDW = 1799.9514 1-4 EEL = 23266.5499 RESTRAINT = 0.0000 ESURF = 181.4637 minimization completed, ENE= -.10689297E+05 RMS= 0.174668E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0817E+04 1.7291E+01 1.1234E+02 C 6982 BOND = 1419.7149 ANGLE = 3762.7074 DIHED = 5374.7396 VDWAALS = -3914.5599 EEL = -35095.7661 EGB = -7618.6471 1-4 VDW = 1787.5794 1-4 EEL = 23286.7245 RESTRAINT = 0.0000 ESURF = 180.4413 minimization completed, ENE= -.10817066E+05 RMS= 0.172910E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0808E+04 1.7308E+01 1.1101E+02 C 1006 BOND = 1387.7930 ANGLE = 3764.3379 DIHED = 5366.0682 VDWAALS = -3912.3925 EEL = -35078.2566 EGB = -7572.8125 1-4 VDW = 1798.9134 1-4 EEL = 23257.4930 RESTRAINT = 0.0000 ESURF = 181.1357 minimization completed, ENE= -.10807720E+05 RMS= 0.173083E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0715E+04 1.7545E+01 1.0808E+02 CA 1669 BOND = 1413.8475 ANGLE = 3766.7197 DIHED = 5424.9561 VDWAALS = -3903.8790 EEL = -34911.3129 EGB = -7722.7557 1-4 VDW = 1817.0827 1-4 EEL = 23217.9227 RESTRAINT = 0.0000 ESURF = 182.6333 minimization completed, ENE= -.10714786E+05 RMS= 0.175454E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0769E+04 1.7336E+01 1.1689E+02 CZ 5933 BOND = 1424.1044 ANGLE = 3758.3282 DIHED = 5443.9115 VDWAALS = -3919.2905 EEL = -35119.6053 EGB = -7599.2868 1-4 VDW = 1804.1729 1-4 EEL = 23258.2689 RESTRAINT = 0.0000 ESURF = 180.2409 minimization completed, ENE= -.10769156E+05 RMS= 0.173362E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0773E+04 1.7437E+01 1.0614E+02 C 1156 BOND = 1371.1656 ANGLE = 3742.3677 DIHED = 5413.0240 VDWAALS = -3891.2957 EEL = -35090.0539 EGB = -7638.9374 1-4 VDW = 1816.2740 1-4 EEL = 23323.3035 RESTRAINT = 0.0000 ESURF = 180.8181 minimization completed, ENE= -.10773334E+05 RMS= 0.174368E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0713E+04 1.7223E+01 1.0324E+02 N 4190 BOND = 1430.6259 ANGLE = 3780.6841 DIHED = 5432.8500 VDWAALS = -3930.3215 EEL = -34969.3471 EGB = -7651.5563 1-4 VDW = 1791.9263 1-4 EEL = 23220.0120 RESTRAINT = 0.0000 ESURF = 182.1995 minimization completed, ENE= -.10712927E+05 RMS= 0.172233E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0766E+04 1.7279E+01 1.1079E+02 C 2209 BOND = 1443.0966 ANGLE = 3727.0227 DIHED = 5426.3512 VDWAALS = -3933.3785 EEL = -34960.9639 EGB = -7652.2398 1-4 VDW = 1787.5372 1-4 EEL = 23215.2649 RESTRAINT = 0.0000 ESURF = 181.8063 minimization completed, ENE= -.10765503E+05 RMS= 0.172790E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0784E+04 1.7263E+01 1.1548E+02 N 1895 BOND = 1416.3562 ANGLE = 3805.2688 DIHED = 5380.4022 VDWAALS = -3995.2716 EEL = -35107.0518 EGB = -7535.8638 1-4 VDW = 1823.1957 1-4 EEL = 23249.4716 RESTRAINT = 0.0000 ESURF = 179.8214 minimization completed, ENE= -.10783671E+05 RMS= 0.172633E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0787E+04 1.7337E+01 1.1259E+02 C 420 BOND = 1424.3058 ANGLE = 3746.7479 DIHED = 5396.5451 VDWAALS = -3909.4564 EEL = -35081.7227 EGB = -7651.9301 1-4 VDW = 1788.6221 1-4 EEL = 23319.7300 RESTRAINT = 0.0000 ESURF = 180.3695 minimization completed, ENE= -.10786789E+05 RMS= 0.173374E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0674E+04 1.7341E+01 1.0751E+02 C 1862 BOND = 1444.5498 ANGLE = 3791.2410 DIHED = 5404.6430 VDWAALS = -3883.2298 EEL = -35068.5454 EGB = -7596.1974 1-4 VDW = 1796.1705 1-4 EEL = 23255.7479 RESTRAINT = 0.0000 ESURF = 181.1535 minimization completed, ENE= -.10674467E+05 RMS= 0.173412E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0711E+04 1.7113E+01 1.1128E+02 C 6630 BOND = 1396.5867 ANGLE = 3792.4232 DIHED = 5430.5981 VDWAALS = -3908.3217 EEL = -34899.4230 EGB = -7737.4250 1-4 VDW = 1781.5490 1-4 EEL = 23251.8843 RESTRAINT = 0.0000 ESURF = 180.8107 minimization completed, ENE= -.10711318E+05 RMS= 0.171129E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0860E+04 1.7386E+01 1.2695E+02 N 1158 BOND = 1441.3469 ANGLE = 3741.1342 DIHED = 5369.6389 VDWAALS = -3935.5884 EEL = -34864.0176 EGB = -7813.6231 1-4 VDW = 1763.3723 1-4 EEL = 23255.6314 RESTRAINT = 0.0000 ESURF = 181.8353 minimization completed, ENE= -.10860270E+05 RMS= 0.173857E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0742E+04 1.7150E+01 1.0436E+02 C 372 BOND = 1420.8914 ANGLE = 3735.2440 DIHED = 5451.5719 VDWAALS = -3901.1982 EEL = -34981.1122 EGB = -7701.6529 1-4 VDW = 1794.3150 1-4 EEL = 23259.2247 RESTRAINT = 0.0000 ESURF = 181.1301 minimization completed, ENE= -.10741586E+05 RMS= 0.171504E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 714.61 ( 7.69% of Gen B) | Calc gb diag 5518.39 (59.40% of Gen B) | Calc gb off-diag 3056.86 (32.91% of Gen B) | Gen Born time 9289.86 (100.0% of Nonbo) | Nonbond force 9289.86 (100.0% of Force) | Bond/Angle/Dihedral 8.77 ( 0.09% of Force) | Force time 9298.64 (100.0% of Runmd) | Runmd Time 9298.64 (98.95% of Total) | Other 98.44 ( 1.05% of Total) | Total time 9397.10 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 19:12:36.989 on 10/19/2010 | Setup done at 19:12:40.521 on 10/19/2010 | Run done at 21:49:14.091 on 10/19/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/19/2010 at 19:12:39 [-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 -1.0656E+04 1.7575E+01 1.0632E+02 C 2470 BOND = 1467.2081 ANGLE = 3730.0837 DIHED = 5440.1717 VDWAALS = -3919.6652 EEL = -35173.9630 EGB = -7503.1451 1-4 VDW = 1826.2922 1-4 EEL = 23296.6772 RESTRAINT = 0.0000 ESURF = 180.4840 minimization completed, ENE= -.10655856E+05 RMS= 0.175746E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0731E+04 1.7502E+01 1.2887E+02 C 7116 BOND = 1454.7307 ANGLE = 3725.8223 DIHED = 5401.2357 VDWAALS = -3893.7553 EEL = -35343.8551 EGB = -7341.8057 1-4 VDW = 1822.5069 1-4 EEL = 23265.1123 RESTRAINT = 0.0000 ESURF = 178.9644 minimization completed, ENE= -.10731044E+05 RMS= 0.175022E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0840E+04 1.7433E+01 1.1107E+02 C 5940 BOND = 1428.2523 ANGLE = 3666.4589 DIHED = 5448.9616 VDWAALS = -3963.7631 EEL = -35204.3331 EGB = -7458.0369 1-4 VDW = 1778.5910 1-4 EEL = 23282.6588 RESTRAINT = 0.0000 ESURF = 180.8642 minimization completed, ENE= -.10840346E+05 RMS= 0.174331E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0779E+04 1.7406E+01 1.2325E+02 CA 722 BOND = 1425.1282 ANGLE = 3630.6533 DIHED = 5435.1064 VDWAALS = -3920.8414 EEL = -35096.0858 EGB = -7477.2077 1-4 VDW = 1806.1486 1-4 EEL = 23238.7608 RESTRAINT = 0.0000 ESURF = 179.2038 minimization completed, ENE= -.10779134E+05 RMS= 0.174056E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0740E+04 1.7326E+01 1.2868E+02 C 5492 BOND = 1467.4057 ANGLE = 3733.6467 DIHED = 5415.8233 VDWAALS = -3926.0740 EEL = -35157.5619 EGB = -7447.6894 1-4 VDW = 1800.3251 1-4 EEL = 23193.9203 RESTRAINT = 0.0000 ESURF = 180.3042 minimization completed, ENE= -.10739900E+05 RMS= 0.173261E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0719E+04 1.7284E+01 1.2418E+02 C 6782 BOND = 1430.2214 ANGLE = 3816.2672 DIHED = 5429.6927 VDWAALS = -3923.5451 EEL = -35406.0865 EGB = -7292.7391 1-4 VDW = 1774.0768 1-4 EEL = 23272.4205 RESTRAINT = 0.0000 ESURF = 180.2385 minimization completed, ENE= -.10719454E+05 RMS= 0.172840E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0699E+04 1.7788E+01 1.6022E+02 CA 1315 BOND = 1503.9827 ANGLE = 3760.2186 DIHED = 5423.5759 VDWAALS = -3883.1653 EEL = -35154.9669 EGB = -7538.8565 1-4 VDW = 1756.6105 1-4 EEL = 23253.2885 RESTRAINT = 0.0000 ESURF = 180.4538 minimization completed, ENE= -.10698859E+05 RMS= 0.177876E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0806E+04 1.7287E+01 1.0913E+02 CG 1078 BOND = 1412.5866 ANGLE = 3737.5707 DIHED = 5443.9826 VDWAALS = -3920.1469 EEL = -35198.7662 EGB = -7486.6335 1-4 VDW = 1792.0798 1-4 EEL = 23233.0489 RESTRAINT = 0.0000 ESURF = 179.9778 minimization completed, ENE= -.10806300E+05 RMS= 0.172868E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0713E+04 1.7310E+01 1.2936E+02 CG 4706 BOND = 1384.9976 ANGLE = 3801.1617 DIHED = 5459.3722 VDWAALS = -3938.6396 EEL = -35172.2817 EGB = -7533.0903 1-4 VDW = 1804.9272 1-4 EEL = 23300.5783 RESTRAINT = 0.0000 ESURF = 180.0164 minimization completed, ENE= -.10712958E+05 RMS= 0.173098E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0830E+04 1.7121E+01 9.9302E+01 CA 6448 BOND = 1415.8817 ANGLE = 3691.4795 DIHED = 5440.6923 VDWAALS = -3919.6516 EEL = -35030.7985 EGB = -7728.4796 1-4 VDW = 1794.7020 1-4 EEL = 23323.0854 RESTRAINT = 0.0000 ESURF = 182.8625 minimization completed, ENE= -.10830226E+05 RMS= 0.171211E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0697E+04 1.7502E+01 1.1162E+02 N 775 BOND = 1434.6750 ANGLE = 3790.3741 DIHED = 5416.2163 VDWAALS = -3942.9093 EEL = -35086.1689 EGB = -7555.2492 1-4 VDW = 1793.6849 1-4 EEL = 23271.9447 RESTRAINT = 0.0000 ESURF = 180.8372 minimization completed, ENE= -.10696595E+05 RMS= 0.175017E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0835E+04 1.7191E+01 1.0929E+02 C 1812 BOND = 1433.3500 ANGLE = 3615.5321 DIHED = 5416.3150 VDWAALS = -3882.4144 EEL = -35179.2409 EGB = -7543.7625 1-4 VDW = 1814.9462 1-4 EEL = 23309.1192 RESTRAINT = 0.0000 ESURF = 180.8243 minimization completed, ENE= -.10835331E+05 RMS= 0.171908E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0834E+04 1.7390E+01 1.2858E+02 C 5456 BOND = 1389.1761 ANGLE = 3721.4688 DIHED = 5448.8526 VDWAALS = -3912.9989 EEL = -35220.8004 EGB = -7647.8483 1-4 VDW = 1800.3938 1-4 EEL = 23405.4009 RESTRAINT = 0.0000 ESURF = 182.7007 minimization completed, ENE= -.10833655E+05 RMS= 0.173903E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0790E+04 1.7232E+01 1.3505E+02 CD 1890 BOND = 1439.2731 ANGLE = 3700.0706 DIHED = 5420.9001 VDWAALS = -3928.2131 EEL = -35114.7998 EGB = -7520.2240 1-4 VDW = 1790.8512 1-4 EEL = 23242.9604 RESTRAINT = 0.0000 ESURF = 178.9128 minimization completed, ENE= -.10790269E+05 RMS= 0.172318E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0733E+04 1.7346E+01 1.1946E+02 N 5397 BOND = 1438.3200 ANGLE = 3728.7003 DIHED = 5419.7824 VDWAALS = -3927.5912 EEL = -35126.3524 EGB = -7537.1308 1-4 VDW = 1785.8445 1-4 EEL = 23305.0339 RESTRAINT = 0.0000 ESURF = 180.3465 minimization completed, ENE= -.10733047E+05 RMS= 0.173465E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0724E+04 1.7283E+01 1.1837E+02 CB 4655 BOND = 1362.5167 ANGLE = 3784.8856 DIHED = 5459.9760 VDWAALS = -3935.4489 EEL = -35129.4031 EGB = -7598.1489 1-4 VDW = 1840.3941 1-4 EEL = 23310.1514 RESTRAINT = 0.0000 ESURF = 181.1660 minimization completed, ENE= -.10723911E+05 RMS= 0.172827E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0731E+04 1.7381E+01 1.0905E+02 C 2806 BOND = 1407.5248 ANGLE = 3714.4122 DIHED = 5421.3580 VDWAALS = -3874.7245 EEL = -35044.9849 EGB = -7657.0476 1-4 VDW = 1803.2616 1-4 EEL = 23318.2088 RESTRAINT = 0.0000 ESURF = 180.9938 minimization completed, ENE= -.10730998E+05 RMS= 0.173814E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0705E+04 1.7267E+01 1.1525E+02 CD 5774 BOND = 1412.3483 ANGLE = 3716.6334 DIHED = 5468.6610 VDWAALS = -3921.9570 EEL = -35093.7439 EGB = -7535.0938 1-4 VDW = 1784.9356 1-4 EEL = 23282.4728 RESTRAINT = 0.0000 ESURF = 180.3030 minimization completed, ENE= -.10705441E+05 RMS= 0.172666E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0679E+04 1.7635E+01 1.1116E+02 N 1844 BOND = 1486.3253 ANGLE = 3756.0724 DIHED = 5449.3005 VDWAALS = -3956.3781 EEL = -35291.5026 EGB = -7433.6233 1-4 VDW = 1812.9383 1-4 EEL = 23318.7901 RESTRAINT = 0.0000 ESURF = 178.6217 minimization completed, ENE= -.10679456E+05 RMS= 0.176351E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0734E+04 1.7413E+01 1.1559E+02 C 4374 BOND = 1397.9474 ANGLE = 3812.2420 DIHED = 5401.8822 VDWAALS = -3982.8888 EEL = -35165.9233 EGB = -7420.8279 1-4 VDW = 1788.4099 1-4 EEL = 23256.3279 RESTRAINT = 0.0000 ESURF = 178.5170 minimization completed, ENE= -.10734314E+05 RMS= 0.174132E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0727E+04 1.7253E+01 1.2190E+02 CZ 5139 BOND = 1393.7531 ANGLE = 3716.0484 DIHED = 5438.3630 VDWAALS = -3943.6124 EEL = -34993.8366 EGB = -7620.9688 1-4 VDW = 1828.7515 1-4 EEL = 23273.5572 RESTRAINT = 0.0000 ESURF = 180.6473 minimization completed, ENE= -.10727297E+05 RMS= 0.172532E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0781E+04 1.6973E+01 1.1630E+02 N 2622 BOND = 1348.6250 ANGLE = 3764.3791 DIHED = 5421.7485 VDWAALS = -3928.9643 EEL = -35168.7831 EGB = -7474.9734 1-4 VDW = 1798.9598 1-4 EEL = 23278.1208 RESTRAINT = 0.0000 ESURF = 180.0838 minimization completed, ENE= -.10780804E+05 RMS= 0.169731E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0767E+04 1.7358E+01 1.1592E+02 C 1509 BOND = 1435.2634 ANGLE = 3745.3700 DIHED = 5419.9445 VDWAALS = -3923.7474 EEL = -35108.9291 EGB = -7601.6507 1-4 VDW = 1795.7076 1-4 EEL = 23290.5354 RESTRAINT = 0.0000 ESURF = 180.4353 minimization completed, ENE= -.10767071E+05 RMS= 0.173580E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0777E+04 1.7104E+01 1.2389E+02 C 1828 BOND = 1385.3361 ANGLE = 3725.5878 DIHED = 5421.9753 VDWAALS = -3978.0856 EEL = -35034.1371 EGB = -7591.1487 1-4 VDW = 1808.8444 1-4 EEL = 23307.6406 RESTRAINT = 0.0000 ESURF = 177.2613 minimization completed, ENE= -.10776726E+05 RMS= 0.171045E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0632E+04 1.7451E+01 1.2814E+02 C 4449 BOND = 1396.8139 ANGLE = 3773.5185 DIHED = 5432.5705 VDWAALS = -3903.2190 EEL = -35332.4334 EGB = -7330.5042 1-4 VDW = 1836.2332 1-4 EEL = 23316.4624 RESTRAINT = 0.0000 ESURF = 178.0853 minimization completed, ENE= -.10632473E+05 RMS= 0.174509E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0797E+04 1.7268E+01 1.1232E+02 C 1852 BOND = 1412.2177 ANGLE = 3732.9910 DIHED = 5417.8349 VDWAALS = -3952.7626 EEL = -35242.0393 EGB = -7390.4303 1-4 VDW = 1771.9781 1-4 EEL = 23274.5032 RESTRAINT = 0.0000 ESURF = 178.4889 minimization completed, ENE= -.10797218E+05 RMS= 0.172683E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0782E+04 1.7220E+01 1.2310E+02 C 1119 BOND = 1418.3368 ANGLE = 3729.5675 DIHED = 5440.0919 VDWAALS = -3893.2507 EEL = -35260.7714 EGB = -7458.5905 1-4 VDW = 1802.7554 1-4 EEL = 23259.3558 RESTRAINT = 0.0000 ESURF = 180.8915 minimization completed, ENE= -.10781614E+05 RMS= 0.172201E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0671E+04 1.7656E+01 1.0569E+02 CD 1153 BOND = 1478.0528 ANGLE = 3785.6474 DIHED = 5428.3628 VDWAALS = -3921.9249 EEL = -35267.9155 EGB = -7439.5643 1-4 VDW = 1808.5774 1-4 EEL = 23276.5988 RESTRAINT = 0.0000 ESURF = 181.3623 minimization completed, ENE= -.10670803E+05 RMS= 0.176557E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0778E+04 1.7267E+01 1.2189E+02 C 1325 BOND = 1424.3301 ANGLE = 3730.8713 DIHED = 5433.0322 VDWAALS = -3912.7565 EEL = -35203.0160 EGB = -7492.1876 1-4 VDW = 1790.6979 1-4 EEL = 23268.8647 RESTRAINT = 0.0000 ESURF = 181.8161 minimization completed, ENE= -.10778348E+05 RMS= 0.172675E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0722E+04 1.7336E+01 1.0948E+02 C 642 BOND = 1438.9560 ANGLE = 3723.4678 DIHED = 5439.1061 VDWAALS = -3897.2747 EEL = -35175.1768 EGB = -7555.2347 1-4 VDW = 1834.1337 1-4 EEL = 23287.8828 RESTRAINT = 0.0000 ESURF = 181.8394 minimization completed, ENE= -.10722301E+05 RMS= 0.173364E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0848E+04 1.7309E+01 1.1623E+02 C 2330 BOND = 1457.8458 ANGLE = 3699.2103 DIHED = 5429.3376 VDWAALS = -3971.3037 EEL = -35361.5710 EGB = -7352.5191 1-4 VDW = 1801.0547 1-4 EEL = 23267.2548 RESTRAINT = 0.0000 ESURF = 182.5953 minimization completed, ENE= -.10848095E+05 RMS= 0.173086E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0865E+04 1.7130E+01 1.1811E+02 C 7833 BOND = 1384.0682 ANGLE = 3749.8725 DIHED = 5397.7714 VDWAALS = -3910.9190 EEL = -35291.4064 EGB = -7396.4834 1-4 VDW = 1772.2987 1-4 EEL = 23249.9815 RESTRAINT = 0.0000 ESURF = 179.5768 minimization completed, ENE= -.10865240E+05 RMS= 0.171295E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0714E+04 1.7536E+01 1.4038E+02 C 4840 BOND = 1421.4931 ANGLE = 3752.8200 DIHED = 5425.9492 VDWAALS = -3911.3650 EEL = -35326.8319 EGB = -7346.2252 1-4 VDW = 1843.1312 1-4 EEL = 23247.3541 RESTRAINT = 0.0000 ESURF = 179.9479 minimization completed, ENE= -.10713727E+05 RMS= 0.175359E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0750E+04 1.7129E+01 1.1264E+02 C 1278 BOND = 1352.6154 ANGLE = 3736.5179 DIHED = 5445.1661 VDWAALS = -3884.6138 EEL = -35240.9894 EGB = -7480.1355 1-4 VDW = 1814.9476 1-4 EEL = 23325.8081 RESTRAINT = 0.0000 ESURF = 180.9411 minimization completed, ENE= -.10749742E+05 RMS= 0.171287E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0733E+04 1.7292E+01 1.2539E+02 CA 4756 BOND = 1414.4638 ANGLE = 3800.9046 DIHED = 5399.2266 VDWAALS = -3910.6450 EEL = -35234.6106 EGB = -7521.1782 1-4 VDW = 1786.6553 1-4 EEL = 23350.7417 RESTRAINT = 0.0000 ESURF = 181.3120 minimization completed, ENE= -.10733130E+05 RMS= 0.172920E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0745E+04 1.7427E+01 1.1424E+02 C 3183 BOND = 1427.9388 ANGLE = 3676.9430 DIHED = 5436.7770 VDWAALS = -3879.8070 EEL = -35100.1465 EGB = -7482.2780 1-4 VDW = 1801.9963 1-4 EEL = 23193.3108 RESTRAINT = 0.0000 ESURF = 180.4725 minimization completed, ENE= -.10744793E+05 RMS= 0.174274E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0759E+04 1.7301E+01 1.1588E+02 CG 6506 BOND = 1383.5396 ANGLE = 3737.2997 DIHED = 5400.9374 VDWAALS = -3937.9697 EEL = -35156.1593 EGB = -7475.5996 1-4 VDW = 1827.4004 1-4 EEL = 23282.7273 RESTRAINT = 0.0000 ESURF = 178.8385 minimization completed, ENE= -.10758986E+05 RMS= 0.173013E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0853E+04 1.7318E+01 1.1277E+02 C 5579 BOND = 1390.4079 ANGLE = 3741.1515 DIHED = 5397.0773 VDWAALS = -3945.0171 EEL = -35295.9292 EGB = -7347.0552 1-4 VDW = 1789.7602 1-4 EEL = 23236.9688 RESTRAINT = 0.0000 ESURF = 180.1099 minimization completed, ENE= -.10852526E+05 RMS= 0.173180E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0710E+04 1.7571E+01 1.0537E+02 C 331 BOND = 1466.1921 ANGLE = 3732.7511 DIHED = 5451.8771 VDWAALS = -3907.5155 EEL = -35353.8542 EGB = -7421.0694 1-4 VDW = 1824.4217 1-4 EEL = 23318.8977 RESTRAINT = 0.0000 ESURF = 178.7362 minimization completed, ENE= -.10709563E+05 RMS= 0.175705E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0642E+04 1.7596E+01 1.2530E+02 C 1325 BOND = 1452.0370 ANGLE = 3755.1547 DIHED = 5440.5757 VDWAALS = -3907.4075 EEL = -35075.3745 EGB = -7561.3306 1-4 VDW = 1804.1532 1-4 EEL = 23272.1288 RESTRAINT = 0.0000 ESURF = 177.6411 minimization completed, ENE= -.10642422E+05 RMS= 0.175960E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0842E+04 1.7289E+01 1.2836E+02 C 3923 BOND = 1411.5779 ANGLE = 3697.9103 DIHED = 5425.6940 VDWAALS = -3939.4978 EEL = -35186.7445 EGB = -7489.9693 1-4 VDW = 1795.5614 1-4 EEL = 23264.7692 RESTRAINT = 0.0000 ESURF = 178.4712 minimization completed, ENE= -.10842228E+05 RMS= 0.172889E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0714E+04 1.7347E+01 1.1406E+02 CZ 5412 BOND = 1418.8028 ANGLE = 3825.5801 DIHED = 5407.3104 VDWAALS = -3895.4068 EEL = -35022.5920 EGB = -7683.6788 1-4 VDW = 1806.2883 1-4 EEL = 23250.1781 RESTRAINT = 0.0000 ESURF = 179.5994 minimization completed, ENE= -.10713918E+05 RMS= 0.173471E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0745E+04 1.7281E+01 1.2102E+02 C 235 BOND = 1378.9019 ANGLE = 3776.3413 DIHED = 5409.9604 VDWAALS = -3921.1636 EEL = -34999.8350 EGB = -7646.8782 1-4 VDW = 1810.4497 1-4 EEL = 23269.2909 RESTRAINT = 0.0000 ESURF = 178.3669 minimization completed, ENE= -.10744566E+05 RMS= 0.172812E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0770E+04 1.7232E+01 1.0882E+02 CA 7592 BOND = 1385.8523 ANGLE = 3731.3324 DIHED = 5436.5541 VDWAALS = -3946.3017 EEL = -34987.9431 EGB = -7653.6442 1-4 VDW = 1809.2617 1-4 EEL = 23274.7057 RESTRAINT = 0.0000 ESURF = 180.3649 minimization completed, ENE= -.10769818E+05 RMS= 0.172318E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0720E+04 1.7337E+01 1.1438E+02 C 1509 BOND = 1415.0817 ANGLE = 3704.7504 DIHED = 5422.7679 VDWAALS = -3949.2136 EEL = -34934.6580 EGB = -7609.3765 1-4 VDW = 1811.9885 1-4 EEL = 23239.3120 RESTRAINT = 0.0000 ESURF = 179.6840 minimization completed, ENE= -.10719664E+05 RMS= 0.173370E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0792E+04 1.7496E+01 1.1678E+02 C 3729 BOND = 1404.2618 ANGLE = 3744.2039 DIHED = 5397.6735 VDWAALS = -3946.1658 EEL = -35099.8221 EGB = -7502.0576 1-4 VDW = 1791.8846 1-4 EEL = 23239.7907 RESTRAINT = 0.0000 ESURF = 177.9467 minimization completed, ENE= -.10792284E+05 RMS= 0.174963E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0771E+04 1.7371E+01 1.2503E+02 C 1379 BOND = 1381.3111 ANGLE = 3818.1995 DIHED = 5448.0087 VDWAALS = -3906.1453 EEL = -35176.6580 EGB = -7533.7706 1-4 VDW = 1793.4735 1-4 EEL = 23224.6659 RESTRAINT = 0.0000 ESURF = 179.5575 minimization completed, ENE= -.10771358E+05 RMS= 0.173709E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0767E+04 1.7424E+01 1.2266E+02 CG 2253 BOND = 1434.9621 ANGLE = 3772.9327 DIHED = 5401.4388 VDWAALS = -3915.8862 EEL = -35228.9612 EGB = -7450.2243 1-4 VDW = 1793.6362 1-4 EEL = 23245.9026 RESTRAINT = 0.0000 ESURF = 179.2386 minimization completed, ENE= -.10766961E+05 RMS= 0.174241E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0751E+04 1.7465E+01 1.3567E+02 CD 3794 BOND = 1417.9749 ANGLE = 3784.0998 DIHED = 5451.9914 VDWAALS = -3910.7182 EEL = -35154.1126 EGB = -7531.3331 1-4 VDW = 1800.2046 1-4 EEL = 23209.5414 RESTRAINT = 0.0000 ESURF = 181.1152 minimization completed, ENE= -.10751237E+05 RMS= 0.174653E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0752E+04 1.7351E+01 1.1571E+02 C 5906 BOND = 1377.7455 ANGLE = 3672.5805 DIHED = 5389.0689 VDWAALS = -3871.4864 EEL = -35014.9796 EGB = -7675.2220 1-4 VDW = 1833.2039 1-4 EEL = 23356.6044 RESTRAINT = 0.0000 ESURF = 180.5672 minimization completed, ENE= -.10751918E+05 RMS= 0.173512E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 705.47 ( 7.62% of Gen B) | Calc gb diag 5507.43 (59.50% of Gen B) | Calc gb off-diag 3042.83 (32.88% of Gen B) | Gen Born time 9255.73 (100.0% of Nonbo) | Nonbond force 9255.73 (100.0% of Force) | Bond/Angle/Dihedral 7.86 ( 0.08% of Force) | Force time 9263.60 (100.0% of Runmd) | Runmd Time 9263.60 (99.01% of Total) | Other 92.71 ( 0.99% of Total) | Total time 9356.33 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 19:12:37.338 on 10/19/2010 | Setup done at 19:12:40.340 on 10/19/2010 | Run done at 21:48:33.668 on 10/19/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/19/2010 at 19:12:37 [-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 -1.0755E+04 1.7067E+01 1.0124E+02 PG 7838 BOND = 1407.6247 ANGLE = 3769.6051 DIHED = 5418.7077 VDWAALS = -3953.2933 EEL = -35124.1981 EGB = -7475.6543 1-4 VDW = 1784.6496 1-4 EEL = 23237.9520 RESTRAINT = 0.0000 ESURF = 180.0125 minimization completed, ENE= -.10754594E+05 RMS= 0.170675E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0681E+04 1.7375E+01 1.0567E+02 C 6509 BOND = 1432.4670 ANGLE = 3750.4421 DIHED = 5437.1815 VDWAALS = -3889.1472 EEL = -35095.0881 EGB = -7571.5088 1-4 VDW = 1798.5608 1-4 EEL = 23275.5244 RESTRAINT = 0.0000 ESURF = 180.5022 minimization completed, ENE= -.10681066E+05 RMS= 0.173755E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0629E+04 1.7607E+01 1.0686E+02 CA 1607 BOND = 1430.1799 ANGLE = 3807.8247 DIHED = 5435.5241 VDWAALS = -3900.3882 EEL = -35094.0598 EGB = -7639.7381 1-4 VDW = 1804.7127 1-4 EEL = 23347.4904 RESTRAINT = 0.0000 ESURF = 179.9218 minimization completed, ENE= -.10628533E+05 RMS= 0.176074E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0879E+04 1.7212E+01 1.0353E+02 CD 3073 BOND = 1362.1574 ANGLE = 3677.8410 DIHED = 5405.8943 VDWAALS = -3869.9088 EEL = -35085.6155 EGB = -7629.2011 1-4 VDW = 1775.2194 1-4 EEL = 23303.2305 RESTRAINT = 0.0000 ESURF = 181.2438 minimization completed, ENE= -.10879139E+05 RMS= 0.172119E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0740E+04 1.7614E+01 1.3092E+02 CB 61 BOND = 1473.7352 ANGLE = 3783.1851 DIHED = 5399.6765 VDWAALS = -3943.6451 EEL = -35080.8036 EGB = -7618.2457 1-4 VDW = 1788.7732 1-4 EEL = 23274.7596 RESTRAINT = 0.0000 ESURF = 182.2783 minimization completed, ENE= -.10740287E+05 RMS= 0.176145E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0795E+04 1.7075E+01 1.0723E+02 C 7833 BOND = 1399.6037 ANGLE = 3674.7332 DIHED = 5427.0784 VDWAALS = -3981.3286 EEL = -35012.3172 EGB = -7705.9100 1-4 VDW = 1825.2494 1-4 EEL = 23397.4637 RESTRAINT = 0.0000 ESURF = 180.4296 minimization completed, ENE= -.10794998E+05 RMS= 0.170750E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0870E+04 1.7186E+01 9.9036E+01 CG 1674 BOND = 1419.5810 ANGLE = 3672.6633 DIHED = 5426.7101 VDWAALS = -3906.8656 EEL = -35065.7571 EGB = -7695.6526 1-4 VDW = 1761.9386 1-4 EEL = 23336.1322 RESTRAINT = 0.0000 ESURF = 181.0239 minimization completed, ENE= -.10870226E+05 RMS= 0.171857E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0715E+04 1.7524E+01 1.3626E+02 N 7146 BOND = 1427.8231 ANGLE = 3722.2382 DIHED = 5419.7744 VDWAALS = -3933.2314 EEL = -35157.4611 EGB = -7562.9608 1-4 VDW = 1823.2659 1-4 EEL = 23365.0309 RESTRAINT = 0.0000 ESURF = 180.4331 minimization completed, ENE= -.10715088E+05 RMS= 0.175243E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0818E+04 1.7166E+01 1.1141E+02 CD 7204 BOND = 1398.3750 ANGLE = 3733.7355 DIHED = 5385.2492 VDWAALS = -3890.3809 EEL = -35326.6401 EGB = -7393.6965 1-4 VDW = 1802.2238 1-4 EEL = 23293.6859 RESTRAINT = 0.0000 ESURF = 179.0250 minimization completed, ENE= -.10818423E+05 RMS= 0.171661E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0834E+04 1.7228E+01 1.1618E+02 C 285 BOND = 1413.8763 ANGLE = 3716.8646 DIHED = 5427.6258 VDWAALS = -3951.7335 EEL = -35245.0204 EGB = -7475.8367 1-4 VDW = 1792.7331 1-4 EEL = 23307.5183 RESTRAINT = 0.0000 ESURF = 180.2699 minimization completed, ENE= -.10833702E+05 RMS= 0.172281E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0894E+04 1.7049E+01 1.1569E+02 N 939 BOND = 1352.8699 ANGLE = 3692.8260 DIHED = 5389.4272 VDWAALS = -3946.4028 EEL = -35158.9808 EGB = -7576.3959 1-4 VDW = 1808.9079 1-4 EEL = 23362.9944 RESTRAINT = 0.0000 ESURF = 181.1060 minimization completed, ENE= -.10893648E+05 RMS= 0.170492E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0780E+04 1.7087E+01 1.1578E+02 C 5059 BOND = 1413.9932 ANGLE = 3760.6135 DIHED = 5426.8172 VDWAALS = -3906.8616 EEL = -34948.9646 EGB = -7722.5696 1-4 VDW = 1786.0009 1-4 EEL = 23229.4987 RESTRAINT = 0.0000 ESURF = 181.6076 minimization completed, ENE= -.10779865E+05 RMS= 0.170870E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0719E+04 1.7354E+01 1.2579E+02 C 3729 BOND = 1430.0298 ANGLE = 3817.1148 DIHED = 5367.5480 VDWAALS = -3880.6713 EEL = -35241.9731 EGB = -7523.8733 1-4 VDW = 1812.0508 1-4 EEL = 23319.1218 RESTRAINT = 0.0000 ESURF = 181.8284 minimization completed, ENE= -.10718824E+05 RMS= 0.173545E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0766E+04 1.7036E+01 1.0216E+02 C 6389 BOND = 1370.5119 ANGLE = 3787.9206 DIHED = 5372.5621 VDWAALS = -3911.8398 EEL = -34942.0797 EGB = -7728.3769 1-4 VDW = 1794.6688 1-4 EEL = 23307.0993 RESTRAINT = 0.0000 ESURF = 183.1699 minimization completed, ENE= -.10766364E+05 RMS= 0.170358E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0728E+04 1.7310E+01 1.2547E+02 C 2142 BOND = 1431.9124 ANGLE = 3786.7448 DIHED = 5438.6261 VDWAALS = -3977.4978 EEL = -34874.3820 EGB = -7820.1902 1-4 VDW = 1804.4326 1-4 EEL = 23299.7941 RESTRAINT = 0.0000 ESURF = 182.9187 minimization completed, ENE= -.10727641E+05 RMS= 0.173101E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0716E+04 1.7201E+01 1.0651E+02 C 2601 BOND = 1380.9124 ANGLE = 3778.2864 DIHED = 5444.0309 VDWAALS = -3905.0966 EEL = -34925.8310 EGB = -7760.8437 1-4 VDW = 1806.2095 1-4 EEL = 23284.1374 RESTRAINT = 0.0000 ESURF = 182.6769 minimization completed, ENE= -.10715518E+05 RMS= 0.172008E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0809E+04 1.7308E+01 1.1878E+02 CA 1722 BOND = 1394.8104 ANGLE = 3707.5020 DIHED = 5418.8620 VDWAALS = -3945.6762 EEL = -35032.3776 EGB = -7660.2644 1-4 VDW = 1811.1121 1-4 EEL = 23314.9050 RESTRAINT = 0.0000 ESURF = 181.7896 minimization completed, ENE= -.10809337E+05 RMS= 0.173079E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0794E+04 1.7053E+01 9.8946E+01 C 4921 BOND = 1415.3592 ANGLE = 3695.7712 DIHED = 5412.7894 VDWAALS = -3920.0156 EEL = -35111.5579 EGB = -7597.3827 1-4 VDW = 1808.3871 1-4 EEL = 23320.4333 RESTRAINT = 0.0000 ESURF = 181.9785 minimization completed, ENE= -.10794238E+05 RMS= 0.170530E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0710E+04 1.7469E+01 1.2069E+02 C 1502 BOND = 1444.3766 ANGLE = 3764.6245 DIHED = 5402.2932 VDWAALS = -3942.0058 EEL = -34986.4823 EGB = -7622.6840 1-4 VDW = 1800.9410 1-4 EEL = 23246.1998 RESTRAINT = 0.0000 ESURF = 183.1051 minimization completed, ENE= -.10709632E+05 RMS= 0.174694E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0716E+04 1.7298E+01 1.2036E+02 C 5983 BOND = 1462.5088 ANGLE = 3731.5373 DIHED = 5468.8748 VDWAALS = -3966.8277 EEL = -34940.7427 EGB = -7698.0595 1-4 VDW = 1770.2119 1-4 EEL = 23274.8137 RESTRAINT = 0.0000 ESURF = 182.0393 minimization completed, ENE= -.10715644E+05 RMS= 0.172982E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0824E+04 1.7199E+01 1.2141E+02 C 2689 BOND = 1429.4512 ANGLE = 3682.2685 DIHED = 5390.4330 VDWAALS = -3904.0582 EEL = -35267.4461 EGB = -7420.5609 1-4 VDW = 1791.3551 1-4 EEL = 23294.2018 RESTRAINT = 0.0000 ESURF = 179.9656 minimization completed, ENE= -.10824390E+05 RMS= 0.171993E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0736E+04 1.7446E+01 1.1218E+02 C 43 BOND = 1430.8888 ANGLE = 3769.9847 DIHED = 5439.6933 VDWAALS = -3939.7622 EEL = -35079.3224 EGB = -7569.2730 1-4 VDW = 1780.3487 1-4 EEL = 23250.9887 RESTRAINT = 0.0000 ESURF = 180.0339 minimization completed, ENE= -.10736420E+05 RMS= 0.174457E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0771E+04 1.7093E+01 1.0764E+02 C 5638 BOND = 1350.8725 ANGLE = 3803.2586 DIHED = 5423.7293 VDWAALS = -3882.4371 EEL = -35379.0428 EGB = -7374.8079 1-4 VDW = 1774.4551 1-4 EEL = 23328.8207 RESTRAINT = 0.0000 ESURF = 183.6639 minimization completed, ENE= -.10771488E+05 RMS= 0.170930E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0804E+04 1.7406E+01 1.0768E+02 C 3907 BOND = 1420.3857 ANGLE = 3714.3573 DIHED = 5420.2179 VDWAALS = -3936.1952 EEL = -35262.7840 EGB = -7500.8429 1-4 VDW = 1814.6740 1-4 EEL = 23343.4925 RESTRAINT = 0.0000 ESURF = 182.3238 minimization completed, ENE= -.10804371E+05 RMS= 0.174061E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0734E+04 1.7413E+01 1.0673E+02 N 5849 BOND = 1446.8173 ANGLE = 3752.3676 DIHED = 5417.0129 VDWAALS = -3895.2068 EEL = -35315.6230 EGB = -7388.0518 1-4 VDW = 1785.1460 1-4 EEL = 23282.7531 RESTRAINT = 0.0000 ESURF = 180.4365 minimization completed, ENE= -.10734348E+05 RMS= 0.174127E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0770E+04 1.7366E+01 1.1453E+02 CA 3065 BOND = 1370.2612 ANGLE = 3736.1631 DIHED = 5433.4905 VDWAALS = -3876.8040 EEL = -35278.8618 EGB = -7477.1522 1-4 VDW = 1820.2576 1-4 EEL = 23320.9824 RESTRAINT = 0.0000 ESURF = 181.4955 minimization completed, ENE= -.10770168E+05 RMS= 0.173655E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0835E+04 1.7164E+01 1.2406E+02 C 1893 BOND = 1380.9855 ANGLE = 3718.4763 DIHED = 5425.1639 VDWAALS = -3934.3612 EEL = -35355.9866 EGB = -7387.4883 1-4 VDW = 1802.7623 1-4 EEL = 23334.7151 RESTRAINT = 0.0000 ESURF = 180.8879 minimization completed, ENE= -.10834845E+05 RMS= 0.171643E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0749E+04 1.7354E+01 1.1752E+02 C 490 BOND = 1410.6813 ANGLE = 3729.1250 DIHED = 5451.6690 VDWAALS = -3919.0660 EEL = -35116.1478 EGB = -7549.4539 1-4 VDW = 1801.1220 1-4 EEL = 23262.9436 RESTRAINT = 0.0000 ESURF = 180.2588 minimization completed, ENE= -.10748868E+05 RMS= 0.173542E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0815E+04 1.7269E+01 1.2189E+02 C 1978 BOND = 1402.0720 ANGLE = 3711.5434 DIHED = 5388.9869 VDWAALS = -3950.9066 EEL = -35140.8014 EGB = -7570.7722 1-4 VDW = 1821.1847 1-4 EEL = 23343.8731 RESTRAINT = 0.0000 ESURF = 180.0263 minimization completed, ENE= -.10814794E+05 RMS= 0.172688E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0741E+04 1.7217E+01 1.1793E+02 N 2622 BOND = 1445.3378 ANGLE = 3780.1834 DIHED = 5390.6181 VDWAALS = -4009.9518 EEL = -35057.6429 EGB = -7536.1949 1-4 VDW = 1776.1104 1-4 EEL = 23290.5323 RESTRAINT = 0.0000 ESURF = 179.7555 minimization completed, ENE= -.10741252E+05 RMS= 0.172165E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0809E+04 1.7175E+01 1.1439E+02 C 5475 BOND = 1395.2667 ANGLE = 3788.7160 DIHED = 5369.2219 VDWAALS = -3977.9554 EEL = -35172.0696 EGB = -7458.7113 1-4 VDW = 1790.9383 1-4 EEL = 23275.2174 RESTRAINT = 0.0000 ESURF = 180.2137 minimization completed, ENE= -.10809162E+05 RMS= 0.171749E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0773E+04 1.7385E+01 1.0989E+02 C 5456 BOND = 1402.8536 ANGLE = 3727.7062 DIHED = 5431.7749 VDWAALS = -3898.7072 EEL = -35144.6004 EGB = -7642.3265 1-4 VDW = 1792.0194 1-4 EEL = 23374.8987 RESTRAINT = 0.0000 ESURF = 182.9805 minimization completed, ENE= -.10773401E+05 RMS= 0.173855E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0826E+04 1.7251E+01 1.1433E+02 C 1878 BOND = 1419.2798 ANGLE = 3663.0878 DIHED = 5431.4163 VDWAALS = -3907.5314 EEL = -35085.1933 EGB = -7635.3989 1-4 VDW = 1791.0876 1-4 EEL = 23313.7141 RESTRAINT = 0.0000 ESURF = 183.1638 minimization completed, ENE= -.10826374E+05 RMS= 0.172510E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0730E+04 1.7454E+01 1.1516E+02 C 4895 BOND = 1421.8390 ANGLE = 3776.1846 DIHED = 5406.3252 VDWAALS = -3896.3437 EEL = -35222.5753 EGB = -7499.5974 1-4 VDW = 1783.5311 1-4 EEL = 23320.2655 RESTRAINT = 0.0000 ESURF = 180.3257 minimization completed, ENE= -.10730045E+05 RMS= 0.174536E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0899E+04 1.7064E+01 1.0415E+02 CA 1219 BOND = 1377.5554 ANGLE = 3690.4599 DIHED = 5393.0295 VDWAALS = -3961.0452 EEL = -35334.5411 EGB = -7400.7511 1-4 VDW = 1807.4058 1-4 EEL = 23350.2447 RESTRAINT = 0.0000 ESURF = 178.9280 minimization completed, ENE= -.10898714E+05 RMS= 0.170638E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0792E+04 1.7366E+01 1.1988E+02 C 5507 BOND = 1430.1226 ANGLE = 3740.0632 DIHED = 5398.7075 VDWAALS = -3932.3296 EEL = -35175.5165 EGB = -7443.1609 1-4 VDW = 1786.1878 1-4 EEL = 23225.0392 RESTRAINT = 0.0000 ESURF = 178.9543 minimization completed, ENE= -.10791932E+05 RMS= 0.173655E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0805E+04 1.7130E+01 1.0763E+02 CG 2732 BOND = 1398.1448 ANGLE = 3684.6197 DIHED = 5406.6177 VDWAALS = -3892.9284 EEL = -35209.0609 EGB = -7550.0672 1-4 VDW = 1814.2199 1-4 EEL = 23364.4859 RESTRAINT = 0.0000 ESURF = 179.1177 minimization completed, ENE= -.10804851E+05 RMS= 0.171300E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0836E+04 1.7056E+01 9.6045E+01 C 6451 BOND = 1372.7912 ANGLE = 3725.5596 DIHED = 5411.6748 VDWAALS = -3953.1933 EEL = -35187.1105 EGB = -7515.3422 1-4 VDW = 1818.9360 1-4 EEL = 23311.4244 RESTRAINT = 0.0000 ESURF = 178.9577 minimization completed, ENE= -.10836302E+05 RMS= 0.170557E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0813E+04 1.7379E+01 1.4383E+02 C 7010 BOND = 1398.7983 ANGLE = 3742.0199 DIHED = 5398.5583 VDWAALS = -3912.3073 EEL = -35191.1341 EGB = -7517.3904 1-4 VDW = 1785.9378 1-4 EEL = 23303.5679 RESTRAINT = 0.0000 ESURF = 178.7809 minimization completed, ENE= -.10813169E+05 RMS= 0.173788E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0863E+04 1.7087E+01 1.1584E+02 N 4132 BOND = 1375.9675 ANGLE = 3725.7598 DIHED = 5414.3657 VDWAALS = -3942.2850 EEL = -35147.9551 EGB = -7610.3688 1-4 VDW = 1808.5211 1-4 EEL = 23332.8256 RESTRAINT = 0.0000 ESURF = 179.8401 minimization completed, ENE= -.10863329E+05 RMS= 0.170865E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0655E+04 1.7452E+01 1.1794E+02 N 3049 BOND = 1463.5015 ANGLE = 3782.0555 DIHED = 5418.2176 VDWAALS = -3877.5011 EEL = -35215.0542 EGB = -7563.8028 1-4 VDW = 1805.0352 1-4 EEL = 23351.3283 RESTRAINT = 0.0000 ESURF = 181.2321 minimization completed, ENE= -.10654988E+05 RMS= 0.174520E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0729E+04 1.7561E+01 1.1493E+02 N 1061 BOND = 1492.5189 ANGLE = 3732.4281 DIHED = 5414.2936 VDWAALS = -3905.1396 EEL = -35023.5168 EGB = -7728.8270 1-4 VDW = 1783.7447 1-4 EEL = 23323.2655 RESTRAINT = 0.0000 ESURF = 182.6999 minimization completed, ENE= -.10728533E+05 RMS= 0.175610E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0699E+04 1.7401E+01 1.0876E+02 CG 143 BOND = 1430.4210 ANGLE = 3726.9451 DIHED = 5450.5796 VDWAALS = -3889.8829 EEL = -35174.7501 EGB = -7530.6340 1-4 VDW = 1791.4250 1-4 EEL = 23316.2247 RESTRAINT = 0.0000 ESURF = 180.4771 minimization completed, ENE= -.10699194E+05 RMS= 0.174008E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0688E+04 1.7398E+01 1.0342E+02 C 2613 BOND = 1461.7031 ANGLE = 3747.7386 DIHED = 5432.3242 VDWAALS = -3957.4803 EEL = -35117.1047 EGB = -7502.0237 1-4 VDW = 1802.5021 1-4 EEL = 23263.6643 RESTRAINT = 0.0000 ESURF = 180.9517 minimization completed, ENE= -.10687725E+05 RMS= 0.173981E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0781E+04 1.7463E+01 9.8392E+01 CG 7383 BOND = 1446.6243 ANGLE = 3770.1574 DIHED = 5421.0189 VDWAALS = -3932.8361 EEL = -35309.5993 EGB = -7400.6789 1-4 VDW = 1769.4786 1-4 EEL = 23273.5893 RESTRAINT = 0.0000 ESURF = 180.8550 minimization completed, ENE= -.10781391E+05 RMS= 0.174627E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0755E+04 1.7252E+01 1.1080E+02 CG 4904 BOND = 1428.5230 ANGLE = 3691.7008 DIHED = 5455.6897 VDWAALS = -3907.2484 EEL = -35413.6979 EGB = -7399.1388 1-4 VDW = 1794.7346 1-4 EEL = 23415.0547 RESTRAINT = 0.0000 ESURF = 179.7852 minimization completed, ENE= -.10754597E+05 RMS= 0.172523E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0785E+04 1.7219E+01 1.1208E+02 CG 52 BOND = 1393.0632 ANGLE = 3725.4909 DIHED = 5455.9958 VDWAALS = -3943.7407 EEL = -35253.1157 EGB = -7394.0497 1-4 VDW = 1796.4744 1-4 EEL = 23253.5267 RESTRAINT = 0.0000 ESURF = 181.3969 minimization completed, ENE= -.10784958E+05 RMS= 0.172194E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0702E+04 1.7487E+01 1.1777E+02 N 2974 BOND = 1443.2558 ANGLE = 3722.7478 DIHED = 5391.2093 VDWAALS = -3926.1828 EEL = -35016.0696 EGB = -7510.3681 1-4 VDW = 1807.1117 1-4 EEL = 23204.4520 RESTRAINT = 0.0000 ESURF = 181.5316 minimization completed, ENE= -.10702312E+05 RMS= 0.174868E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0789E+04 1.7337E+01 1.1638E+02 C 1398 BOND = 1392.8874 ANGLE = 3714.6836 DIHED = 5412.4783 VDWAALS = -3967.8355 EEL = -35053.4341 EGB = -7620.0200 1-4 VDW = 1794.8162 1-4 EEL = 23357.9857 RESTRAINT = 0.0000 ESURF = 179.5118 minimization completed, ENE= -.10788927E+05 RMS= 0.173375E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0714E+04 1.7195E+01 1.1044E+02 N 7760 BOND = 1406.8609 ANGLE = 3684.1468 DIHED = 5443.2699 VDWAALS = -3866.4226 EEL = -35167.7774 EGB = -7510.3003 1-4 VDW = 1829.7988 1-4 EEL = 23284.0722 RESTRAINT = 0.0000 ESURF = 182.3248 minimization completed, ENE= -.10714027E+05 RMS= 0.171953E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 699.93 ( 7.60% of Gen B) | Calc gb diag 5493.78 (59.68% of Gen B) | Calc gb off-diag 3012.12 (32.72% of Gen B) | Gen Born time 9205.83 (100.0% of Nonbo) | Nonbond force 9205.83 (100.0% of Force) | Bond/Angle/Dihedral 6.93 ( 0.08% of Force) | Force time 9212.77 (100.0% of Runmd) | Runmd Time 9212.77 (99.08% of Total) | Other 85.84 ( 0.92% of Total) | Total time 9298.64 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 19:12:36.939 on 10/19/2010 | Setup done at 19:12:38.679 on 10/19/2010 | Run done at 21:47:35.577 on 10/19/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/19/2010 at 19:12:37 [-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 -1.0734E+04 1.7303E+01 9.8585E+01 C 5557 BOND = 1438.2803 ANGLE = 3749.9052 DIHED = 5414.5034 VDWAALS = -3935.0626 EEL = -34896.7979 EGB = -7782.6463 1-4 VDW = 1785.9399 1-4 EEL = 23311.1736 RESTRAINT = 0.0000 ESURF = 180.6331 minimization completed, ENE= -.10734071E+05 RMS= 0.173026E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0717E+04 1.7417E+01 1.1953E+02 C 3923 BOND = 1380.6719 ANGLE = 3703.0357 DIHED = 5465.5525 VDWAALS = -3933.5578 EEL = -35015.6349 EGB = -7622.9317 1-4 VDW = 1817.0417 1-4 EEL = 23310.3769 RESTRAINT = 0.0000 ESURF = 178.6146 minimization completed, ENE= -.10716831E+05 RMS= 0.174175E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0776E+04 1.7276E+01 1.1487E+02 C 4752 BOND = 1389.2794 ANGLE = 3678.4092 DIHED = 5446.2844 VDWAALS = -3923.8143 EEL = -34927.1892 EGB = -7665.6797 1-4 VDW = 1805.9899 1-4 EEL = 23240.5941 RESTRAINT = 0.0000 ESURF = 179.9329 minimization completed, ENE= -.10776193E+05 RMS= 0.172760E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0776E+04 1.7197E+01 1.2242E+02 C 5557 BOND = 1396.5108 ANGLE = 3768.4077 DIHED = 5357.8667 VDWAALS = -3951.4241 EEL = -34872.6119 EGB = -7737.7472 1-4 VDW = 1808.7410 1-4 EEL = 23275.3936 RESTRAINT = 0.0000 ESURF = 178.5472 minimization completed, ENE= -.10776316E+05 RMS= 0.171972E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0762E+04 1.7255E+01 1.1892E+02 CZ 5225 BOND = 1405.9892 ANGLE = 3733.4070 DIHED = 5401.8494 VDWAALS = -3944.9478 EEL = -34832.9506 EGB = -7818.5012 1-4 VDW = 1803.3506 1-4 EEL = 23309.5287 RESTRAINT = 0.0000 ESURF = 180.2815 minimization completed, ENE= -.10761993E+05 RMS= 0.172549E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0701E+04 1.7271E+01 1.0770E+02 C 2041 BOND = 1430.9313 ANGLE = 3744.1460 DIHED = 5389.8531 VDWAALS = -3910.1773 EEL = -34898.4782 EGB = -7719.7032 1-4 VDW = 1825.2146 1-4 EEL = 23255.7104 RESTRAINT = 0.0000 ESURF = 181.4545 minimization completed, ENE= -.10701049E+05 RMS= 0.172709E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0805E+04 1.7184E+01 1.1807E+02 N 5864 BOND = 1382.5095 ANGLE = 3679.0810 DIHED = 5450.9200 VDWAALS = -3900.3341 EEL = -35063.9277 EGB = -7645.4702 1-4 VDW = 1809.5359 1-4 EEL = 23303.5659 RESTRAINT = 0.0000 ESURF = 179.1520 minimization completed, ENE= -.10804968E+05 RMS= 0.171843E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0680E+04 1.7200E+01 1.1475E+02 C 2179 BOND = 1355.4855 ANGLE = 3838.5601 DIHED = 5415.3105 VDWAALS = -3900.2698 EEL = -34961.8568 EGB = -7695.5926 1-4 VDW = 1797.6076 1-4 EEL = 23288.8039 RESTRAINT = 0.0000 ESURF = 181.5619 minimization completed, ENE= -.10680390E+05 RMS= 0.172004E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0788E+04 1.7314E+01 1.1219E+02 CA 3278 BOND = 1394.1141 ANGLE = 3790.4585 DIHED = 5400.6709 VDWAALS = -3930.1819 EEL = -34967.0841 EGB = -7674.2676 1-4 VDW = 1790.4565 1-4 EEL = 23228.0365 RESTRAINT = 0.0000 ESURF = 180.2797 minimization completed, ENE= -.10787517E+05 RMS= 0.173142E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0764E+04 1.7341E+01 1.3110E+02 CB 442 BOND = 1385.9674 ANGLE = 3742.6427 DIHED = 5418.2863 VDWAALS = -3903.7680 EEL = -35096.8109 EGB = -7568.2956 1-4 VDW = 1782.9017 1-4 EEL = 23295.3045 RESTRAINT = 0.0000 ESURF = 179.7234 minimization completed, ENE= -.10764049E+05 RMS= 0.173412E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0752E+04 1.7172E+01 1.0445E+02 C 6143 BOND = 1418.5196 ANGLE = 3606.6845 DIHED = 5402.6167 VDWAALS = -3913.3024 EEL = -34886.8069 EGB = -7713.0325 1-4 VDW = 1832.8463 1-4 EEL = 23317.5049 RESTRAINT = 0.0000 ESURF = 182.6311 minimization completed, ENE= -.10752339E+05 RMS= 0.171717E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0756E+04 1.7310E+01 1.1403E+02 C 1182 BOND = 1419.4943 ANGLE = 3769.5647 DIHED = 5432.0025 VDWAALS = -3947.3636 EEL = -34914.1550 EGB = -7687.8491 1-4 VDW = 1766.6158 1-4 EEL = 23226.6181 RESTRAINT = 0.0000 ESURF = 178.6764 minimization completed, ENE= -.10756396E+05 RMS= 0.173101E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0693E+04 1.7329E+01 1.1712E+02 CD 2268 BOND = 1390.1676 ANGLE = 3786.4445 DIHED = 5409.8900 VDWAALS = -3862.7272 EEL = -35223.8891 EGB = -7467.3600 1-4 VDW = 1815.0230 1-4 EEL = 23279.1053 RESTRAINT = 0.0000 ESURF = 180.4206 minimization completed, ENE= -.10692925E+05 RMS= 0.173292E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0847E+04 1.6944E+01 1.1394E+02 C 6526 BOND = 1402.7151 ANGLE = 3694.9264 DIHED = 5449.2000 VDWAALS = -3906.6836 EEL = -35196.0806 EGB = -7460.2505 1-4 VDW = 1785.0207 1-4 EEL = 23203.6856 RESTRAINT = 0.0000 ESURF = 180.4217 minimization completed, ENE= -.10847045E+05 RMS= 0.169445E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0726E+04 1.7439E+01 1.2505E+02 C 4568 BOND = 1443.0637 ANGLE = 3663.7448 DIHED = 5466.8710 VDWAALS = -3881.8092 EEL = -35173.0769 EGB = -7466.3710 1-4 VDW = 1813.4720 1-4 EEL = 23228.0353 RESTRAINT = 0.0000 ESURF = 180.2243 minimization completed, ENE= -.10725846E+05 RMS= 0.174389E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0813E+04 1.7289E+01 1.0903E+02 C 3617 BOND = 1404.1302 ANGLE = 3710.1874 DIHED = 5489.8917 VDWAALS = -3911.6132 EEL = -35125.2229 EGB = -7597.0709 1-4 VDW = 1787.4925 1-4 EEL = 23246.6037 RESTRAINT = 0.0000 ESURF = 182.1424 minimization completed, ENE= -.10813459E+05 RMS= 0.172894E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0704E+04 1.7327E+01 1.1219E+02 C 3359 BOND = 1430.0402 ANGLE = 3731.4593 DIHED = 5387.9448 VDWAALS = -3937.9574 EEL = -34982.9583 EGB = -7746.6594 1-4 VDW = 1828.8079 1-4 EEL = 23404.4783 RESTRAINT = 0.0000 ESURF = 181.2983 minimization completed, ENE= -.10703546E+05 RMS= 0.173267E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0725E+04 1.7571E+01 1.2901E+02 CG 1287 BOND = 1432.9841 ANGLE = 3714.0646 DIHED = 5393.0672 VDWAALS = -3897.3187 EEL = -34947.5059 EGB = -7713.4233 1-4 VDW = 1785.4386 1-4 EEL = 23327.7314 RESTRAINT = 0.0000 ESURF = 180.1762 minimization completed, ENE= -.10724786E+05 RMS= 0.175712E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0798E+04 1.7375E+01 1.0822E+02 C 3782 BOND = 1436.6372 ANGLE = 3729.5263 DIHED = 5391.5003 VDWAALS = -3897.8352 EEL = -35073.7863 EGB = -7640.5049 1-4 VDW = 1786.9722 1-4 EEL = 23286.5376 RESTRAINT = 0.0000 ESURF = 182.5079 minimization completed, ENE= -.10798445E+05 RMS= 0.173750E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0739E+04 1.7536E+01 1.1976E+02 C 5622 BOND = 1436.7601 ANGLE = 3736.7867 DIHED = 5398.6398 VDWAALS = -3901.7691 EEL = -35081.6372 EGB = -7575.3678 1-4 VDW = 1787.9017 1-4 EEL = 23278.7496 RESTRAINT = 0.0000 ESURF = 180.6324 minimization completed, ENE= -.10739304E+05 RMS= 0.175360E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0845E+04 1.7413E+01 1.1481E+02 CA 7182 BOND = 1436.2304 ANGLE = 3721.0628 DIHED = 5409.8135 VDWAALS = -3946.4584 EEL = -35080.9618 EGB = -7616.3157 1-4 VDW = 1788.5291 1-4 EEL = 23262.0731 RESTRAINT = 0.0000 ESURF = 181.4769 minimization completed, ENE= -.10844550E+05 RMS= 0.174126E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0730E+04 1.7466E+01 1.1541E+02 CD 6712 BOND = 1430.8281 ANGLE = 3749.6043 DIHED = 5403.2765 VDWAALS = -3926.8697 EEL = -35109.6855 EGB = -7634.4324 1-4 VDW = 1803.2750 1-4 EEL = 23374.0723 RESTRAINT = 0.0000 ESURF = 180.3604 minimization completed, ENE= -.10729571E+05 RMS= 0.174659E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0825E+04 1.7373E+01 1.1858E+02 CG 6506 BOND = 1429.1387 ANGLE = 3722.5017 DIHED = 5361.9770 VDWAALS = -3923.5539 EEL = -35115.0097 EGB = -7580.7167 1-4 VDW = 1822.4855 1-4 EEL = 23277.2272 RESTRAINT = 0.0000 ESURF = 180.5977 minimization completed, ENE= -.10825353E+05 RMS= 0.173725E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0736E+04 1.7226E+01 1.1431E+02 CD 3135 BOND = 1353.4368 ANGLE = 3757.6546 DIHED = 5406.2233 VDWAALS = -3872.8243 EEL = -35103.5514 EGB = -7556.1269 1-4 VDW = 1784.0906 1-4 EEL = 23312.6802 RESTRAINT = 0.0000 ESURF = 182.1699 minimization completed, ENE= -.10736247E+05 RMS= 0.172259E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0612E+04 1.7519E+01 1.2437E+02 C 1878 BOND = 1435.4788 ANGLE = 3810.9297 DIHED = 5407.5205 VDWAALS = -3902.7251 EEL = -34855.9601 EGB = -7760.0302 1-4 VDW = 1812.5354 1-4 EEL = 23257.9508 RESTRAINT = 0.0000 ESURF = 182.5446 minimization completed, ENE= -.10611756E+05 RMS= 0.175190E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0718E+04 1.7295E+01 1.2594E+02 CE1 2898 BOND = 1431.5165 ANGLE = 3687.1889 DIHED = 5465.3692 VDWAALS = -3930.4215 EEL = -34857.7259 EGB = -7795.4029 1-4 VDW = 1785.4533 1-4 EEL = 23313.3793 RESTRAINT = 0.0000 ESURF = 182.3715 minimization completed, ENE= -.10718272E+05 RMS= 0.172954E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0846E+04 1.7314E+01 1.1383E+02 C 6940 BOND = 1376.1319 ANGLE = 3644.3375 DIHED = 5411.1013 VDWAALS = -3895.3254 EEL = -34878.1992 EGB = -7833.9525 1-4 VDW = 1796.7059 1-4 EEL = 23348.3404 RESTRAINT = 0.0000 ESURF = 185.3323 minimization completed, ENE= -.10845528E+05 RMS= 0.173138E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0723E+04 1.7616E+01 1.4319E+02 C 6982 BOND = 1480.5595 ANGLE = 3777.6604 DIHED = 5402.7894 VDWAALS = -3963.6042 EEL = -34753.1683 EGB = -7884.8464 1-4 VDW = 1779.9842 1-4 EEL = 23253.5221 RESTRAINT = 0.0000 ESURF = 183.8849 minimization completed, ENE= -.10723218E+05 RMS= 0.176164E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0701E+04 1.7410E+01 1.0987E+02 CD 5184 BOND = 1414.7756 ANGLE = 3721.1139 DIHED = 5454.8521 VDWAALS = -3911.5636 EEL = -34893.7609 EGB = -7797.0187 1-4 VDW = 1793.7922 1-4 EEL = 23330.7761 RESTRAINT = 0.0000 ESURF = 185.8601 minimization completed, ENE= -.10701173E+05 RMS= 0.174096E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0818E+04 1.6994E+01 1.1653E+02 CZ 6666 BOND = 1381.5919 ANGLE = 3735.9651 DIHED = 5406.3713 VDWAALS = -3870.2264 EEL = -35034.4202 EGB = -7671.4997 1-4 VDW = 1779.3206 1-4 EEL = 23271.0111 RESTRAINT = 0.0000 ESURF = 184.0280 minimization completed, ENE= -.10817858E+05 RMS= 0.169935E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0821E+04 1.7323E+01 1.1458E+02 CG 4197 BOND = 1411.9819 ANGLE = 3728.9330 DIHED = 5438.3617 VDWAALS = -3938.5033 EEL = -35130.0398 EGB = -7649.8630 1-4 VDW = 1795.8031 1-4 EEL = 23341.2902 RESTRAINT = 0.0000 ESURF = 181.0442 minimization completed, ENE= -.10820992E+05 RMS= 0.173234E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0745E+04 1.7415E+01 1.3078E+02 N 4970 BOND = 1477.7210 ANGLE = 3715.5990 DIHED = 5400.1175 VDWAALS = -3892.2572 EEL = -35050.3661 EGB = -7684.0498 1-4 VDW = 1805.6865 1-4 EEL = 23299.6576 RESTRAINT = 0.0000 ESURF = 183.1807 minimization completed, ENE= -.10744711E+05 RMS= 0.174149E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0763E+04 1.7600E+01 1.2733E+02 C 2823 BOND = 1438.8553 ANGLE = 3688.1459 DIHED = 5432.3670 VDWAALS = -3901.0505 EEL = -35111.7376 EGB = -7531.7937 1-4 VDW = 1785.8767 1-4 EEL = 23258.4032 RESTRAINT = 0.0000 ESURF = 178.2582 minimization completed, ENE= -.10762676E+05 RMS= 0.175996E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0810E+04 1.7141E+01 1.1267E+02 C 2951 BOND = 1383.4972 ANGLE = 3722.8378 DIHED = 5418.9771 VDWAALS = -3901.3038 EEL = -35175.9134 EGB = -7568.6952 1-4 VDW = 1816.9447 1-4 EEL = 23312.7185 RESTRAINT = 0.0000 ESURF = 180.9459 minimization completed, ENE= -.10809991E+05 RMS= 0.171410E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0790E+04 1.7293E+01 1.2643E+02 C 6077 BOND = 1401.7294 ANGLE = 3704.9996 DIHED = 5396.7929 VDWAALS = -3942.2758 EEL = -35138.8118 EGB = -7600.4688 1-4 VDW = 1802.8091 1-4 EEL = 23405.4478 RESTRAINT = 0.0000 ESURF = 179.4241 minimization completed, ENE= -.10790354E+05 RMS= 0.172929E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0729E+04 1.7399E+01 1.0920E+02 C 4495 BOND = 1415.3501 ANGLE = 3782.6662 DIHED = 5410.2200 VDWAALS = -3912.7692 EEL = -35074.6598 EGB = -7631.8161 1-4 VDW = 1819.0610 1-4 EEL = 23281.8459 RESTRAINT = 0.0000 ESURF = 180.9702 minimization completed, ENE= -.10729132E+05 RMS= 0.173986E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0765E+04 1.7381E+01 1.2594E+02 C 964 BOND = 1456.4324 ANGLE = 3751.5400 DIHED = 5380.3264 VDWAALS = -3957.5444 EEL = -35049.0436 EGB = -7581.8823 1-4 VDW = 1790.5232 1-4 EEL = 23264.8478 RESTRAINT = 0.0000 ESURF = 179.7753 minimization completed, ENE= -.10765025E+05 RMS= 0.173809E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0581E+04 1.7484E+01 1.3444E+02 C 1978 BOND = 1454.2169 ANGLE = 3849.6071 DIHED = 5483.0214 VDWAALS = -3910.4104 EEL = -35216.2526 EGB = -7516.0643 1-4 VDW = 1789.7648 1-4 EEL = 23303.3629 RESTRAINT = 0.0000 ESURF = 181.7203 minimization completed, ENE= -.10581034E+05 RMS= 0.174845E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0713E+04 1.7490E+01 1.2914E+02 CG 4342 BOND = 1416.7746 ANGLE = 3730.2930 DIHED = 5425.6663 VDWAALS = -3936.2146 EEL = -35088.2126 EGB = -7596.1606 1-4 VDW = 1829.5265 1-4 EEL = 23323.4167 RESTRAINT = 0.0000 ESURF = 181.6546 minimization completed, ENE= -.10713256E+05 RMS= 0.174903E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0843E+04 1.6970E+01 1.1378E+02 CD 1018 BOND = 1354.3332 ANGLE = 3705.1237 DIHED = 5457.4029 VDWAALS = -3912.7800 EEL = -35109.6115 EGB = -7576.0958 1-4 VDW = 1777.8630 1-4 EEL = 23278.7257 RESTRAINT = 0.0000 ESURF = 181.7389 minimization completed, ENE= -.10843300E+05 RMS= 0.169705E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0750E+04 1.7403E+01 1.1369E+02 CG 1629 BOND = 1406.4180 ANGLE = 3784.5364 DIHED = 5408.2714 VDWAALS = -3961.1057 EEL = -35181.4504 EGB = -7501.2514 1-4 VDW = 1796.1183 1-4 EEL = 23315.5830 RESTRAINT = 0.0000 ESURF = 182.4650 minimization completed, ENE= -.10750415E+05 RMS= 0.174034E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0830E+04 1.7180E+01 1.0726E+02 CG 552 BOND = 1414.6435 ANGLE = 3633.3230 DIHED = 5431.8173 VDWAALS = -3975.3225 EEL = -35234.1684 EGB = -7407.5250 1-4 VDW = 1812.9057 1-4 EEL = 23313.2048 RESTRAINT = 0.0000 ESURF = 180.8280 minimization completed, ENE= -.10830293E+05 RMS= 0.171803E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0663E+04 1.7594E+01 1.0864E+02 C 5738 BOND = 1435.4664 ANGLE = 3782.2020 DIHED = 5409.6651 VDWAALS = -3891.3373 EEL = -35294.9274 EGB = -7401.0747 1-4 VDW = 1817.6546 1-4 EEL = 23297.3685 RESTRAINT = 0.0000 ESURF = 181.7174 minimization completed, ENE= -.10663266E+05 RMS= 0.175941E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0739E+04 1.7356E+01 1.2461E+02 CG 2960 BOND = 1402.3952 ANGLE = 3761.6735 DIHED = 5424.0047 VDWAALS = -3890.3290 EEL = -35388.1324 EGB = -7392.3910 1-4 VDW = 1798.8853 1-4 EEL = 23364.5044 RESTRAINT = 0.0000 ESURF = 180.2712 minimization completed, ENE= -.10739118E+05 RMS= 0.173565E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0827E+04 1.7209E+01 1.1500E+02 CG 782 BOND = 1382.0059 ANGLE = 3721.8944 DIHED = 5362.1704 VDWAALS = -3887.0981 EEL = -35303.3698 EGB = -7440.4284 1-4 VDW = 1830.9300 1-4 EEL = 23325.2842 RESTRAINT = 0.0000 ESURF = 181.3861 minimization completed, ENE= -.10827225E+05 RMS= 0.172090E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0808E+04 1.7146E+01 1.1898E+02 N 2679 BOND = 1413.7893 ANGLE = 3711.2982 DIHED = 5404.6342 VDWAALS = -3928.3773 EEL = -35190.0420 EGB = -7478.0448 1-4 VDW = 1785.8916 1-4 EEL = 23292.7841 RESTRAINT = 0.0000 ESURF = 180.2861 minimization completed, ENE= -.10807781E+05 RMS= 0.171458E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0881E+04 1.7288E+01 1.1305E+02 CZ 862 BOND = 1423.8001 ANGLE = 3652.4589 DIHED = 5387.5620 VDWAALS = -3922.5297 EEL = -35159.1319 EGB = -7611.6330 1-4 VDW = 1799.6764 1-4 EEL = 23366.3324 RESTRAINT = 0.0000 ESURF = 182.1455 minimization completed, ENE= -.10881319E+05 RMS= 0.172878E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0847E+04 1.7190E+01 1.1388E+02 CZ 5225 BOND = 1384.8981 ANGLE = 3735.1237 DIHED = 5413.5937 VDWAALS = -3926.2539 EEL = -35185.4841 EGB = -7550.8244 1-4 VDW = 1791.9542 1-4 EEL = 23308.6730 RESTRAINT = 0.0000 ESURF = 181.0273 minimization completed, ENE= -.10847292E+05 RMS= 0.171898E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0690E+04 1.7440E+01 1.2470E+02 C 372 BOND = 1433.8799 ANGLE = 3743.6359 DIHED = 5371.7712 VDWAALS = -3906.9676 EEL = -35072.8084 EGB = -7537.8936 1-4 VDW = 1810.2188 1-4 EEL = 23287.0170 RESTRAINT = 0.0000 ESURF = 181.2639 minimization completed, ENE= -.10689883E+05 RMS= 0.174395E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0795E+04 1.7529E+01 1.2351E+02 C 1379 BOND = 1459.8124 ANGLE = 3724.0746 DIHED = 5372.5603 VDWAALS = -3961.6042 EEL = -35100.6346 EGB = -7563.7620 1-4 VDW = 1766.9583 1-4 EEL = 23327.3581 RESTRAINT = 0.0000 ESURF = 180.1203 minimization completed, ENE= -.10795117E+05 RMS= 0.175288E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 716.18 ( 7.76% of Gen B) | Calc gb diag 5470.02 (59.24% of Gen B) | Calc gb off-diag 3047.33 (33.00% of Gen B) | Gen Born time 9233.53 (100.0% of Nonbo) | Nonbond force 9233.53 (100.0% of Force) | Bond/Angle/Dihedral 5.96 ( 0.06% of Force) | Force time 9239.49 (100.0% of Runmd) | Runmd Time 9239.49 (98.99% of Total) | Other 94.54 ( 1.01% of Total) | Total time 9334.05 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 19:12:36.558 on 10/19/2010 | Setup done at 19:12:38.739 on 10/19/2010 | Run done at 21:48:10.611 on 10/19/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/19/2010 at 19:12:36 [-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 -1.0802E+04 1.7118E+01 1.1039E+02 N 1650 BOND = 1412.7164 ANGLE = 3695.6055 DIHED = 5406.6534 VDWAALS = -3976.6723 EEL = -34829.4993 EGB = -7802.6307 1-4 VDW = 1823.0710 1-4 EEL = 23288.5531 RESTRAINT = 0.0000 ESURF = 180.0534 minimization completed, ENE= -.10802149E+05 RMS= 0.171185E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0820E+04 1.7183E+01 1.1022E+02 N 5024 BOND = 1425.5258 ANGLE = 3728.9664 DIHED = 5412.3011 VDWAALS = -3944.4480 EEL = -35033.3426 EGB = -7693.9899 1-4 VDW = 1795.9736 1-4 EEL = 23308.6513 RESTRAINT = 0.0000 ESURF = 180.1242 minimization completed, ENE= -.10820238E+05 RMS= 0.171830E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0743E+04 1.7390E+01 1.1043E+02 C 5738 BOND = 1393.1515 ANGLE = 3793.9863 DIHED = 5415.9810 VDWAALS = -3939.3746 EEL = -35041.6355 EGB = -7654.1604 1-4 VDW = 1788.1486 1-4 EEL = 23322.8197 RESTRAINT = 0.0000 ESURF = 177.9435 minimization completed, ENE= -.10743140E+05 RMS= 0.173902E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0795E+04 1.7145E+01 1.1907E+02 C 1103 BOND = 1418.5820 ANGLE = 3718.3514 DIHED = 5427.7118 VDWAALS = -3920.6838 EEL = -34954.1307 EGB = -7727.2506 1-4 VDW = 1781.9872 1-4 EEL = 23280.9037 RESTRAINT = 0.0000 ESURF = 180.0013 minimization completed, ENE= -.10794528E+05 RMS= 0.171447E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0754E+04 1.7256E+01 1.1614E+02 CG 6506 BOND = 1453.5368 ANGLE = 3733.0978 DIHED = 5453.3740 VDWAALS = -3886.5375 EEL = -35022.4828 EGB = -7730.8067 1-4 VDW = 1784.1053 1-4 EEL = 23280.5472 RESTRAINT = 0.0000 ESURF = 180.8891 minimization completed, ENE= -.10754277E+05 RMS= 0.172564E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0712E+04 1.7259E+01 1.1927E+02 C 1182 BOND = 1390.6477 ANGLE = 3787.0528 DIHED = 5418.4749 VDWAALS = -3890.5307 EEL = -34839.1533 EGB = -7873.1920 1-4 VDW = 1804.7857 1-4 EEL = 23306.1510 RESTRAINT = 0.0000 ESURF = 184.0443 minimization completed, ENE= -.10711720E+05 RMS= 0.172589E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0611E+04 1.7622E+01 1.2305E+02 C 398 BOND = 1475.2520 ANGLE = 3755.6352 DIHED = 5444.6658 VDWAALS = -3980.2574 EEL = -34884.9360 EGB = -7761.9388 1-4 VDW = 1826.7519 1-4 EEL = 23332.5018 RESTRAINT = 0.0000 ESURF = 181.6141 minimization completed, ENE= -.10610711E+05 RMS= 0.176217E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0666E+04 1.7546E+01 1.1207E+02 C 2308 BOND = 1424.9378 ANGLE = 3799.7544 DIHED = 5394.3496 VDWAALS = -3958.3309 EEL = -34957.0804 EGB = -7727.2392 1-4 VDW = 1828.0787 1-4 EEL = 23348.9316 RESTRAINT = 0.0000 ESURF = 180.5887 minimization completed, ENE= -.10666010E+05 RMS= 0.175460E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0798E+04 1.7348E+01 1.3571E+02 C 5884 BOND = 1449.3681 ANGLE = 3670.4678 DIHED = 5415.4416 VDWAALS = -3923.1190 EEL = -35078.7273 EGB = -7576.6789 1-4 VDW = 1800.2112 1-4 EEL = 23266.4374 RESTRAINT = 0.0000 ESURF = 178.6649 minimization completed, ENE= -.10797934E+05 RMS= 0.173478E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0816E+04 1.7333E+01 1.3162E+02 CD 5859 BOND = 1389.7666 ANGLE = 3688.2596 DIHED = 5423.3002 VDWAALS = -3998.3527 EEL = -35122.9164 EGB = -7516.0544 1-4 VDW = 1830.4764 1-4 EEL = 23310.2854 RESTRAINT = 0.0000 ESURF = 178.8374 minimization completed, ENE= -.10816398E+05 RMS= 0.173328E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0751E+04 1.7212E+01 1.0002E+02 CG 617 BOND = 1363.0035 ANGLE = 3738.1278 DIHED = 5431.0865 VDWAALS = -3922.2763 EEL = -35094.5717 EGB = -7588.4792 1-4 VDW = 1815.2555 1-4 EEL = 23325.1861 RESTRAINT = 0.0000 ESURF = 181.2894 minimization completed, ENE= -.10751379E+05 RMS= 0.172123E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0687E+04 1.7399E+01 1.1580E+02 C 773 BOND = 1401.4947 ANGLE = 3806.5960 DIHED = 5402.0234 VDWAALS = -3898.2281 EEL = -35159.4816 EGB = -7479.1967 1-4 VDW = 1826.9070 1-4 EEL = 23231.5781 RESTRAINT = 0.0000 ESURF = 181.2260 minimization completed, ENE= -.10687081E+05 RMS= 0.173993E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0749E+04 1.7455E+01 1.2249E+02 CA 1315 BOND = 1443.5485 ANGLE = 3747.3047 DIHED = 5396.4777 VDWAALS = -3956.1351 EEL = -35076.5400 EGB = -7679.7718 1-4 VDW = 1807.0056 1-4 EEL = 23386.7496 RESTRAINT = 0.0000 ESURF = 181.9056 minimization completed, ENE= -.10749455E+05 RMS= 0.174553E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0797E+04 1.7414E+01 1.0687E+02 N 6558 BOND = 1412.7744 ANGLE = 3687.9702 DIHED = 5433.2193 VDWAALS = -3928.8804 EEL = -35109.3181 EGB = -7571.1089 1-4 VDW = 1794.4172 1-4 EEL = 23304.6699 RESTRAINT = 0.0000 ESURF = 178.9885 minimization completed, ENE= -.10797268E+05 RMS= 0.174143E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0731E+04 1.7354E+01 1.1817E+02 N 6998 BOND = 1382.6691 ANGLE = 3746.9054 DIHED = 5424.4047 VDWAALS = -3928.8798 EEL = -35085.1818 EGB = -7633.5193 1-4 VDW = 1822.5589 1-4 EEL = 23358.7096 RESTRAINT = 0.0000 ESURF = 181.3269 minimization completed, ENE= -.10731006E+05 RMS= 0.173544E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0771E+04 1.7279E+01 1.1835E+02 CA 5742 BOND = 1439.3569 ANGLE = 3821.0478 DIHED = 5430.8159 VDWAALS = -3929.2968 EEL = -34998.9517 EGB = -7697.8233 1-4 VDW = 1748.6501 1-4 EEL = 23233.5789 RESTRAINT = 0.0000 ESURF = 181.7233 minimization completed, ENE= -.10770899E+05 RMS= 0.172789E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0782E+04 1.7286E+01 1.3054E+02 CD 2818 BOND = 1404.3261 ANGLE = 3762.3311 DIHED = 5426.7154 VDWAALS = -3918.3378 EEL = -35219.3544 EGB = -7498.8245 1-4 VDW = 1793.3078 1-4 EEL = 23289.0709 RESTRAINT = 0.0000 ESURF = 178.5479 minimization completed, ENE= -.10782218E+05 RMS= 0.172859E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0843E+04 1.6863E+01 1.2180E+02 CD 5244 BOND = 1337.2905 ANGLE = 3748.8848 DIHED = 5381.6438 VDWAALS = -3947.5051 EEL = -34995.2538 EGB = -7650.0947 1-4 VDW = 1788.4401 1-4 EEL = 23314.8459 RESTRAINT = 0.0000 ESURF = 178.2625 minimization completed, ENE= -.10843486E+05 RMS= 0.168627E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0801E+04 1.7185E+01 1.1457E+02 CD 1905 BOND = 1407.4993 ANGLE = 3699.2430 DIHED = 5383.1282 VDWAALS = -3890.8155 EEL = -34925.2180 EGB = -7710.5588 1-4 VDW = 1777.3508 1-4 EEL = 23277.3880 RESTRAINT = 0.0000 ESURF = 181.4094 minimization completed, ENE= -.10800574E+05 RMS= 0.171854E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0765E+04 1.7351E+01 1.1261E+02 C 2843 BOND = 1420.0170 ANGLE = 3732.2504 DIHED = 5396.9965 VDWAALS = -3909.5340 EEL = -35059.0702 EGB = -7600.2370 1-4 VDW = 1782.1216 1-4 EEL = 23291.4573 RESTRAINT = 0.0000 ESURF = 180.7428 minimization completed, ENE= -.10765256E+05 RMS= 0.173507E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0752E+04 1.7206E+01 1.0672E+02 C 6317 BOND = 1424.8427 ANGLE = 3673.5213 DIHED = 5454.8246 VDWAALS = -3896.8532 EEL = -35051.0623 EGB = -7586.9073 1-4 VDW = 1788.3216 1-4 EEL = 23260.9455 RESTRAINT = 0.0000 ESURF = 180.7587 minimization completed, ENE= -.10751608E+05 RMS= 0.172062E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0790E+04 1.7272E+01 1.3478E+02 CD 3816 BOND = 1440.5680 ANGLE = 3685.0757 DIHED = 5422.5287 VDWAALS = -3924.2118 EEL = -35074.5841 EGB = -7555.8774 1-4 VDW = 1789.4931 1-4 EEL = 23248.6275 RESTRAINT = 0.0000 ESURF = 178.7616 minimization completed, ENE= -.10789619E+05 RMS= 0.172717E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0702E+04 1.7108E+01 1.1039E+02 C 2806 BOND = 1397.6591 ANGLE = 3755.3977 DIHED = 5423.4417 VDWAALS = -3903.2824 EEL = -34972.5518 EGB = -7636.7247 1-4 VDW = 1792.6616 1-4 EEL = 23261.2430 RESTRAINT = 0.0000 ESURF = 180.0704 minimization completed, ENE= -.10702085E+05 RMS= 0.171083E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0772E+04 1.7384E+01 1.2109E+02 C6 7863 BOND = 1439.5450 ANGLE = 3620.7356 DIHED = 5466.6788 VDWAALS = -3932.9691 EEL = -35018.2238 EGB = -7653.8166 1-4 VDW = 1818.1104 1-4 EEL = 23308.9894 RESTRAINT = 0.0000 ESURF = 178.7069 minimization completed, ENE= -.10772243E+05 RMS= 0.173845E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0854E+04 1.7042E+01 1.1462E+02 CG 995 BOND = 1352.0912 ANGLE = 3743.0766 DIHED = 5372.5621 VDWAALS = -3955.2834 EEL = -34904.7156 EGB = -7786.7507 1-4 VDW = 1787.5057 1-4 EEL = 23357.3006 RESTRAINT = 0.0000 ESURF = 180.5753 minimization completed, ENE= -.10853638E+05 RMS= 0.170421E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0700E+04 1.7136E+01 1.0302E+02 C 2271 BOND = 1438.3961 ANGLE = 3757.5320 DIHED = 5444.7942 VDWAALS = -3945.9859 EEL = -35030.8793 EGB = -7669.4604 1-4 VDW = 1791.5163 1-4 EEL = 23333.0046 RESTRAINT = 0.0000 ESURF = 180.9173 minimization completed, ENE= -.10700165E+05 RMS= 0.171363E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0831E+04 1.7500E+01 1.3989E+02 C 7264 BOND = 1447.5928 ANGLE = 3697.8892 DIHED = 5377.7004 VDWAALS = -3951.2160 EEL = -35028.9650 EGB = -7560.9574 1-4 VDW = 1770.9630 1-4 EEL = 23237.7380 RESTRAINT = 0.0000 ESURF = 178.0203 minimization completed, ENE= -.10831235E+05 RMS= 0.174997E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0699E+04 1.7249E+01 1.1602E+02 CZ 3420 BOND = 1451.9375 ANGLE = 3711.7006 DIHED = 5414.4877 VDWAALS = -3937.7845 EEL = -34969.9374 EGB = -7609.0490 1-4 VDW = 1795.4050 1-4 EEL = 23263.8959 RESTRAINT = 0.0000 ESURF = 180.8247 minimization completed, ENE= -.10698519E+05 RMS= 0.172487E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0827E+04 1.7216E+01 1.2085E+02 C 884 BOND = 1447.1847 ANGLE = 3662.6767 DIHED = 5402.9917 VDWAALS = -3940.1952 EEL = -35034.9042 EGB = -7618.0546 1-4 VDW = 1771.3375 1-4 EEL = 23302.7179 RESTRAINT = 0.0000 ESURF = 179.4340 minimization completed, ENE= -.10826811E+05 RMS= 0.172165E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0777E+04 1.7358E+01 1.0854E+02 C 7281 BOND = 1443.9722 ANGLE = 3739.4024 DIHED = 5414.9713 VDWAALS = -3961.5049 EEL = -35094.0313 EGB = -7574.5275 1-4 VDW = 1792.8338 1-4 EEL = 23282.9920 RESTRAINT = 0.0000 ESURF = 179.1766 minimization completed, ENE= -.10776716E+05 RMS= 0.173582E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0855E+04 1.7155E+01 1.1511E+02 C 7632 BOND = 1446.2473 ANGLE = 3604.3107 DIHED = 5396.7470 VDWAALS = -3933.5999 EEL = -35119.4241 EGB = -7534.7091 1-4 VDW = 1809.0318 1-4 EEL = 23296.3985 RESTRAINT = 0.0000 ESURF = 179.6240 minimization completed, ENE= -.10855374E+05 RMS= 0.171553E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0687E+04 1.7193E+01 1.1075E+02 C 7511 BOND = 1383.5475 ANGLE = 3830.0048 DIHED = 5415.1749 VDWAALS = -3926.4729 EEL = -35197.8142 EGB = -7456.5938 1-4 VDW = 1797.9465 1-4 EEL = 23286.9091 RESTRAINT = 0.0000 ESURF = 180.6988 minimization completed, ENE= -.10686599E+05 RMS= 0.171929E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0776E+04 1.7172E+01 1.1291E+02 C 2233 BOND = 1371.8181 ANGLE = 3736.5570 DIHED = 5454.0278 VDWAALS = -3945.5571 EEL = -35019.7746 EGB = -7589.2078 1-4 VDW = 1785.2639 1-4 EEL = 23252.0260 RESTRAINT = 0.0000 ESURF = 178.8709 minimization completed, ENE= -.10775976E+05 RMS= 0.171723E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0576E+04 1.7437E+01 1.2963E+02 C 6683 BOND = 1417.3703 ANGLE = 3789.1731 DIHED = 5442.4892 VDWAALS = -3903.3530 EEL = -34987.9187 EGB = -7608.7221 1-4 VDW = 1803.4541 1-4 EEL = 23289.8183 RESTRAINT = 0.0000 ESURF = 181.2835 minimization completed, ENE= -.10576405E+05 RMS= 0.174374E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0646E+04 1.7461E+01 1.2091E+02 CD 5297 BOND = 1463.4899 ANGLE = 3846.9055 DIHED = 5435.9312 VDWAALS = -3970.3020 EEL = -34994.3049 EGB = -7621.3613 1-4 VDW = 1793.6946 1-4 EEL = 23219.5818 RESTRAINT = 0.0000 ESURF = 180.2192 minimization completed, ENE= -.10646146E+05 RMS= 0.174612E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0647E+04 1.7397E+01 1.2157E+02 CG 2429 BOND = 1433.5692 ANGLE = 3769.2725 DIHED = 5458.6579 VDWAALS = -3943.6199 EEL = -34926.2746 EGB = -7789.2405 1-4 VDW = 1835.2652 1-4 EEL = 23335.4923 RESTRAINT = 0.0000 ESURF = 180.3774 minimization completed, ENE= -.10646501E+05 RMS= 0.173969E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0672E+04 1.7356E+01 1.2111E+02 C 2378 BOND = 1398.4679 ANGLE = 3772.8580 DIHED = 5414.5059 VDWAALS = -3947.7576 EEL = -34855.3601 EGB = -7736.3032 1-4 VDW = 1818.8186 1-4 EEL = 23282.3139 RESTRAINT = 0.0000 ESURF = 180.3329 minimization completed, ENE= -.10672124E+05 RMS= 0.173561E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0744E+04 1.7400E+01 1.1261E+02 C 4840 BOND = 1455.4541 ANGLE = 3746.0749 DIHED = 5413.2686 VDWAALS = -3923.9827 EEL = -35048.4631 EGB = -7702.1742 1-4 VDW = 1794.4563 1-4 EEL = 23341.3800 RESTRAINT = 0.0000 ESURF = 179.7924 minimization completed, ENE= -.10744194E+05 RMS= 0.174000E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0694E+04 1.7314E+01 1.1493E+02 C 2125 BOND = 1396.5986 ANGLE = 3800.3264 DIHED = 5454.6478 VDWAALS = -3987.0883 EEL = -34813.3319 EGB = -7801.4484 1-4 VDW = 1777.6686 1-4 EEL = 23298.3406 RESTRAINT = 0.0000 ESURF = 179.9636 minimization completed, ENE= -.10694323E+05 RMS= 0.173141E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0706E+04 1.7617E+01 1.0287E+02 C 845 BOND = 1478.0782 ANGLE = 3738.2657 DIHED = 5407.2529 VDWAALS = -3923.2520 EEL = -35038.3431 EGB = -7693.6529 1-4 VDW = 1777.1854 1-4 EEL = 23367.4180 RESTRAINT = 0.0000 ESURF = 180.7019 minimization completed, ENE= -.10706346E+05 RMS= 0.176166E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0675E+04 1.7277E+01 1.0693E+02 C 2723 BOND = 1404.4817 ANGLE = 3796.3632 DIHED = 5452.6855 VDWAALS = -3969.4524 EEL = -34870.2789 EGB = -7781.1329 1-4 VDW = 1805.0911 1-4 EEL = 23306.4780 RESTRAINT = 0.0000 ESURF = 180.4086 minimization completed, ENE= -.10675356E+05 RMS= 0.172767E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0726E+04 1.7406E+01 1.2940E+02 CD 949 BOND = 1430.8994 ANGLE = 3713.1665 DIHED = 5435.4858 VDWAALS = -3970.6121 EEL = -34920.7453 EGB = -7670.4845 1-4 VDW = 1777.9046 1-4 EEL = 23299.4769 RESTRAINT = 0.0000 ESURF = 179.3287 minimization completed, ENE= -.10725580E+05 RMS= 0.174064E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0736E+04 1.7220E+01 1.1240E+02 CB 6689 BOND = 1372.9391 ANGLE = 3759.9079 DIHED = 5359.1816 VDWAALS = -3981.4804 EEL = -34942.6152 EGB = -7615.9331 1-4 VDW = 1820.9718 1-4 EEL = 23311.1768 RESTRAINT = 0.0000 ESURF = 180.1493 minimization completed, ENE= -.10735702E+05 RMS= 0.172201E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0710E+04 1.7401E+01 1.4846E+02 C 3172 BOND = 1431.6952 ANGLE = 3739.9763 DIHED = 5404.0953 VDWAALS = -3918.2110 EEL = -35056.0507 EGB = -7567.9471 1-4 VDW = 1781.3826 1-4 EEL = 23295.1234 RESTRAINT = 0.0000 ESURF = 179.6222 minimization completed, ENE= -.10710314E+05 RMS= 0.174011E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0702E+04 1.7451E+01 1.0741E+02 PA 7846 BOND = 1394.6822 ANGLE = 3778.6392 DIHED = 5469.0585 VDWAALS = -3937.5439 EEL = -34942.6416 EGB = -7763.5523 1-4 VDW = 1815.0796 1-4 EEL = 23305.0431 RESTRAINT = 0.0000 ESURF = 179.0051 minimization completed, ENE= -.10702230E+05 RMS= 0.174515E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0623E+04 1.7552E+01 1.0951E+02 C 3552 BOND = 1453.0648 ANGLE = 3750.9843 DIHED = 5447.0582 VDWAALS = -3887.0817 EEL = -34956.0147 EGB = -7735.6234 1-4 VDW = 1817.5256 1-4 EEL = 23307.9254 RESTRAINT = 0.0000 ESURF = 179.0420 minimization completed, ENE= -.10623120E+05 RMS= 0.175519E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0664E+04 1.7629E+01 1.0090E+02 N 6089 BOND = 1458.9548 ANGLE = 3729.8818 DIHED = 5436.8661 VDWAALS = -3917.1880 EEL = -34905.0344 EGB = -7762.1739 1-4 VDW = 1833.0878 1-4 EEL = 23284.7968 RESTRAINT = 0.0000 ESURF = 176.8496 minimization completed, ENE= -.10663959E+05 RMS= 0.176286E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0705E+04 1.7413E+01 1.1923E+02 C 952 BOND = 1418.0231 ANGLE = 3811.1266 DIHED = 5395.0768 VDWAALS = -3908.3913 EEL = -34916.0074 EGB = -7755.8207 1-4 VDW = 1793.2057 1-4 EEL = 23279.0075 RESTRAINT = 0.0000 ESURF = 178.4595 minimization completed, ENE= -.10705320E+05 RMS= 0.174126E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0811E+04 1.7281E+01 1.2001E+02 CD 6463 BOND = 1392.0504 ANGLE = 3742.0229 DIHED = 5425.4619 VDWAALS = -3944.9479 EEL = -35049.2094 EGB = -7671.2123 1-4 VDW = 1794.2815 1-4 EEL = 23322.8219 RESTRAINT = 0.0000 ESURF = 178.1120 minimization completed, ENE= -.10810619E+05 RMS= 0.172809E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0735E+04 1.7231E+01 1.1132E+02 CG 3763 BOND = 1407.4455 ANGLE = 3722.5436 DIHED = 5427.2395 VDWAALS = -3922.7201 EEL = -34837.4595 EGB = -7788.9231 1-4 VDW = 1816.4986 1-4 EEL = 23260.2885 RESTRAINT = 0.0000 ESURF = 179.9628 minimization completed, ENE= -.10735124E+05 RMS= 0.172306E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 731.65 ( 7.84% of Gen B) | Calc gb diag 5516.99 (59.13% of Gen B) | Calc gb off-diag 3080.98 (33.02% of Gen B) | Gen Born time 9329.61 (100.0% of Nonbo) | Nonbond force 9329.61 (100.0% of Force) | Bond/Angle/Dihedral 7.27 ( 0.08% of Force) | Force time 9336.89 (100.0% of Runmd) | Runmd Time 9336.89 (99.04% of Total) | Other 90.13 ( 0.96% of Total) | Total time 9427.04 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 19:12:36.561 on 10/19/2010 | Setup done at 19:12:37.815 on 10/19/2010 | Run done at 21:49:43.597 on 10/19/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/19/2010 at 19:12:36 [-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 -1.0805E+04 1.7284E+01 1.1274E+02 CZ 3420 BOND = 1397.5716 ANGLE = 3732.0397 DIHED = 5401.1197 VDWAALS = -3878.1996 EEL = -35036.2401 EGB = -7663.4135 1-4 VDW = 1797.0537 1-4 EEL = 23258.7295 RESTRAINT = 0.0000 ESURF = 185.8458 minimization completed, ENE= -.10805493E+05 RMS= 0.172844E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0665E+04 1.7482E+01 1.3634E+02 C 7081 BOND = 1432.4416 ANGLE = 3751.8470 DIHED = 5471.8978 VDWAALS = -3947.9718 EEL = -35049.2985 EGB = -7658.7559 1-4 VDW = 1801.3957 1-4 EEL = 23349.0616 RESTRAINT = 0.0000 ESURF = 183.9162 minimization completed, ENE= -.10665466E+05 RMS= 0.174818E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0693E+04 1.7443E+01 1.1972E+02 NE 5522 BOND = 1424.3256 ANGLE = 3819.9717 DIHED = 5432.7501 VDWAALS = -3905.9908 EEL = -35068.9805 EGB = -7602.9982 1-4 VDW = 1766.3721 1-4 EEL = 23257.2793 RESTRAINT = 0.0000 ESURF = 184.4591 minimization completed, ENE= -.10692812E+05 RMS= 0.174433E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0721E+04 1.7337E+01 1.2036E+02 C 4435 BOND = 1403.0564 ANGLE = 3646.5072 DIHED = 5441.6809 VDWAALS = -3861.3513 EEL = -35119.1752 EGB = -7555.6790 1-4 VDW = 1834.2034 1-4 EEL = 23306.0427 RESTRAINT = 0.0000 ESURF = 183.5196 minimization completed, ENE= -.10721195E+05 RMS= 0.173372E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0746E+04 1.7427E+01 1.0625E+02 CD 6712 BOND = 1433.9007 ANGLE = 3741.0825 DIHED = 5414.6835 VDWAALS = -3864.9515 EEL = -35125.7560 EGB = -7566.0360 1-4 VDW = 1785.8729 1-4 EEL = 23250.7498 RESTRAINT = 0.0000 ESURF = 184.5315 minimization completed, ENE= -.10745922E+05 RMS= 0.174266E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0812E+04 1.7352E+01 1.1945E+02 N 2679 BOND = 1460.2641 ANGLE = 3650.7204 DIHED = 5461.7030 VDWAALS = -3895.4829 EEL = -35163.9634 EGB = -7565.8989 1-4 VDW = 1796.3522 1-4 EEL = 23258.7689 RESTRAINT = 0.0000 ESURF = 185.3796 minimization completed, ENE= -.10812157E+05 RMS= 0.173522E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0649E+04 1.7312E+01 1.1943E+02 C 6649 BOND = 1417.1823 ANGLE = 3780.8772 DIHED = 5449.0521 VDWAALS = -3852.3895 EEL = -35065.6230 EGB = -7553.2224 1-4 VDW = 1804.7085 1-4 EEL = 23186.3225 RESTRAINT = 0.0000 ESURF = 183.6808 minimization completed, ENE= -.10649412E+05 RMS= 0.173117E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0781E+04 1.7327E+01 1.2826E+02 C 350 BOND = 1410.9659 ANGLE = 3746.1165 DIHED = 5388.9935 VDWAALS = -3885.1099 EEL = -35133.7291 EGB = -7562.6248 1-4 VDW = 1786.5978 1-4 EEL = 23285.2720 RESTRAINT = 0.0000 ESURF = 182.7330 minimization completed, ENE= -.10780785E+05 RMS= 0.173266E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0626E+04 1.7365E+01 1.1246E+02 N 3185 BOND = 1427.4311 ANGLE = 3821.3420 DIHED = 5419.5135 VDWAALS = -3881.0117 EEL = -35147.8652 EGB = -7502.2143 1-4 VDW = 1813.1835 1-4 EEL = 23240.1760 RESTRAINT = 0.0000 ESURF = 183.8567 minimization completed, ENE= -.10625588E+05 RMS= 0.173649E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0753E+04 1.7316E+01 1.0402E+02 C 1052 BOND = 1420.8198 ANGLE = 3782.9998 DIHED = 5421.1479 VDWAALS = -3942.0834 EEL = -35198.3982 EGB = -7515.8310 1-4 VDW = 1794.5585 1-4 EEL = 23299.4781 RESTRAINT = 0.0000 ESURF = 183.9940 minimization completed, ENE= -.10753315E+05 RMS= 0.173164E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0731E+04 1.7291E+01 1.2599E+02 C 751 BOND = 1424.0317 ANGLE = 3713.9543 DIHED = 5396.3552 VDWAALS = -3910.7720 EEL = -35195.4843 EGB = -7404.5002 1-4 VDW = 1802.4576 1-4 EEL = 23261.0041 RESTRAINT = 0.0000 ESURF = 181.7095 minimization completed, ENE= -.10731244E+05 RMS= 0.172915E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0785E+04 1.7204E+01 1.1288E+02 C 3107 BOND = 1372.8479 ANGLE = 3752.0974 DIHED = 5432.9057 VDWAALS = -3902.3697 EEL = -35285.4151 EGB = -7397.4667 1-4 VDW = 1783.3156 1-4 EEL = 23276.8489 RESTRAINT = 0.0000 ESURF = 181.8671 minimization completed, ENE= -.10785369E+05 RMS= 0.172036E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0648E+04 1.7635E+01 1.1656E+02 C 2751 BOND = 1441.1721 ANGLE = 3882.5684 DIHED = 5394.1910 VDWAALS = -3926.6261 EEL = -35194.3350 EGB = -7515.2499 1-4 VDW = 1794.5091 1-4 EEL = 23292.3398 RESTRAINT = 0.0000 ESURF = 183.1066 minimization completed, ENE= -.10648324E+05 RMS= 0.176349E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0700E+04 1.7475E+01 1.2196E+02 C 718 BOND = 1465.1004 ANGLE = 3752.1273 DIHED = 5441.3481 VDWAALS = -3857.1317 EEL = -35297.0452 EGB = -7480.9883 1-4 VDW = 1779.1897 1-4 EEL = 23312.6229 RESTRAINT = 0.0000 ESURF = 184.3519 minimization completed, ENE= -.10700425E+05 RMS= 0.174748E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0771E+04 1.7378E+01 1.1664E+02 C 6401 BOND = 1444.8957 ANGLE = 3691.1798 DIHED = 5433.7180 VDWAALS = -3890.6131 EEL = -35241.2319 EGB = -7462.7640 1-4 VDW = 1797.3201 1-4 EEL = 23273.0650 RESTRAINT = 0.0000 ESURF = 183.0797 minimization completed, ENE= -.10771351E+05 RMS= 0.173784E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0677E+04 1.7415E+01 1.1362E+02 C 2937 BOND = 1441.4621 ANGLE = 3780.7990 DIHED = 5435.4078 VDWAALS = -3936.4730 EEL = -35220.8640 EGB = -7537.3073 1-4 VDW = 1846.9291 1-4 EEL = 23330.1004 RESTRAINT = 0.0000 ESURF = 182.7170 minimization completed, ENE= -.10677229E+05 RMS= 0.174147E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0651E+04 1.7392E+01 1.0179E+02 CD 7204 BOND = 1417.8080 ANGLE = 3809.6442 DIHED = 5447.2522 VDWAALS = -3887.8839 EEL = -35164.6082 EGB = -7577.2054 1-4 VDW = 1801.1183 1-4 EEL = 23318.6437 RESTRAINT = 0.0000 ESURF = 184.2084 minimization completed, ENE= -.10651023E+05 RMS= 0.173924E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0703E+04 1.7482E+01 1.2667E+02 CD 7204 BOND = 1419.3641 ANGLE = 3701.3317 DIHED = 5404.7127 VDWAALS = -3859.9327 EEL = -35187.0391 EGB = -7568.2049 1-4 VDW = 1829.8778 1-4 EEL = 23373.4515 RESTRAINT = 0.0000 ESURF = 183.0962 minimization completed, ENE= -.10703343E+05 RMS= 0.174823E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0690E+04 1.7511E+01 1.2048E+02 C 7715 BOND = 1458.1637 ANGLE = 3762.2681 DIHED = 5405.8912 VDWAALS = -3905.7106 EEL = -35209.9241 EGB = -7470.9216 1-4 VDW = 1808.5370 1-4 EEL = 23280.0301 RESTRAINT = 0.0000 ESURF = 182.0721 minimization completed, ENE= -.10689594E+05 RMS= 0.175113E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0774E+04 1.7331E+01 1.3263E+02 C 6673 BOND = 1470.3814 ANGLE = 3665.4999 DIHED = 5419.5717 VDWAALS = -3940.8157 EEL = -35121.0899 EGB = -7496.2802 1-4 VDW = 1814.2092 1-4 EEL = 23229.6084 RESTRAINT = 0.0000 ESURF = 184.9395 minimization completed, ENE= -.10773976E+05 RMS= 0.173308E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0704E+04 1.7422E+01 1.0668E+02 N 478 BOND = 1433.2108 ANGLE = 3764.3101 DIHED = 5439.5997 VDWAALS = -3876.0968 EEL = -35210.2626 EGB = -7495.4472 1-4 VDW = 1788.9047 1-4 EEL = 23267.9834 RESTRAINT = 0.0000 ESURF = 184.0826 minimization completed, ENE= -.10703715E+05 RMS= 0.174221E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0623E+04 1.7361E+01 1.1808E+02 C 3076 BOND = 1471.2634 ANGLE = 3776.8665 DIHED = 5431.3862 VDWAALS = -3945.4985 EEL = -34947.8005 EGB = -7636.6199 1-4 VDW = 1776.8525 1-4 EEL = 23265.4092 RESTRAINT = 0.0000 ESURF = 185.1960 minimization completed, ENE= -.10622945E+05 RMS= 0.173611E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0681E+04 1.7360E+01 1.0623E+02 C 5325 BOND = 1389.1537 ANGLE = 3754.6284 DIHED = 5449.8465 VDWAALS = -3923.2773 EEL = -35071.3704 EGB = -7563.0545 1-4 VDW = 1807.1708 1-4 EEL = 23291.2210 RESTRAINT = 0.0000 ESURF = 185.0656 minimization completed, ENE= -.10680616E+05 RMS= 0.173600E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0710E+04 1.7472E+01 1.1284E+02 C 1425 BOND = 1419.0996 ANGLE = 3788.5812 DIHED = 5417.9825 VDWAALS = -3909.8842 EEL = -34999.8947 EGB = -7722.0745 1-4 VDW = 1797.1959 1-4 EEL = 23314.2627 RESTRAINT = 0.0000 ESURF = 185.1042 minimization completed, ENE= -.10709627E+05 RMS= 0.174721E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0652E+04 1.7415E+01 1.0365E+02 C 1363 BOND = 1427.3444 ANGLE = 3816.4931 DIHED = 5436.7094 VDWAALS = -3903.1351 EEL = -35041.3431 EGB = -7605.9230 1-4 VDW = 1783.2619 1-4 EEL = 23249.6786 RESTRAINT = 0.0000 ESURF = 184.5605 minimization completed, ENE= -.10652353E+05 RMS= 0.174148E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0659E+04 1.7452E+01 1.1387E+02 C 3097 BOND = 1420.8312 ANGLE = 3767.6536 DIHED = 5450.7524 VDWAALS = -3930.8730 EEL = -35052.5462 EGB = -7638.7454 1-4 VDW = 1808.4981 1-4 EEL = 23330.1780 RESTRAINT = 0.0000 ESURF = 185.3191 minimization completed, ENE= -.10658932E+05 RMS= 0.174520E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0721E+04 1.7114E+01 1.0825E+02 N 5707 BOND = 1397.5445 ANGLE = 3668.1618 DIHED = 5414.6934 VDWAALS = -3906.5695 EEL = -35026.9618 EGB = -7648.6895 1-4 VDW = 1839.4001 1-4 EEL = 23357.2044 RESTRAINT = 0.0000 ESURF = 184.0320 minimization completed, ENE= -.10721185E+05 RMS= 0.171144E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0854E+04 1.7334E+01 1.0811E+02 C 6166 BOND = 1409.3248 ANGLE = 3670.6829 DIHED = 5397.7873 VDWAALS = -3922.8324 EEL = -35041.9895 EGB = -7643.4536 1-4 VDW = 1790.9419 1-4 EEL = 23300.6764 RESTRAINT = 0.0000 ESURF = 184.4696 minimization completed, ENE= -.10854393E+05 RMS= 0.173338E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0761E+04 1.7282E+01 1.2001E+02 C 5266 BOND = 1447.8593 ANGLE = 3708.4525 DIHED = 5402.6284 VDWAALS = -3880.0334 EEL = -35045.2641 EGB = -7675.8971 1-4 VDW = 1806.8135 1-4 EEL = 23291.1688 RESTRAINT = 0.0000 ESURF = 183.4728 minimization completed, ENE= -.10760799E+05 RMS= 0.172824E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0692E+04 1.7227E+01 1.1573E+02 C 3011 BOND = 1412.2916 ANGLE = 3772.7967 DIHED = 5439.0402 VDWAALS = -3913.0490 EEL = -35089.2267 EGB = -7531.9199 1-4 VDW = 1795.4287 1-4 EEL = 23238.0846 RESTRAINT = 0.0000 ESURF = 184.1440 minimization completed, ENE= -.10692410E+05 RMS= 0.172268E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0743E+04 1.7060E+01 1.0871E+02 C 2586 BOND = 1420.4828 ANGLE = 3764.2849 DIHED = 5422.1586 VDWAALS = -3920.1297 EEL = -35033.0892 EGB = -7661.7375 1-4 VDW = 1791.6030 1-4 EEL = 23289.8561 RESTRAINT = 0.0000 ESURF = 183.8208 minimization completed, ENE= -.10742750E+05 RMS= 0.170597E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0667E+04 1.7598E+01 1.1790E+02 CD 4522 BOND = 1465.8397 ANGLE = 3782.9102 DIHED = 5381.8270 VDWAALS = -3927.1265 EEL = -35074.0036 EGB = -7550.3285 1-4 VDW = 1802.6265 1-4 EEL = 23270.6285 RESTRAINT = 0.0000 ESURF = 180.2878 minimization completed, ENE= -.10667339E+05 RMS= 0.175984E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0626E+04 1.7440E+01 1.3892E+02 CG 7309 BOND = 1426.8994 ANGLE = 3752.6879 DIHED = 5430.5948 VDWAALS = -3863.4671 EEL = -35064.7066 EGB = -7600.5677 1-4 VDW = 1830.2222 1-4 EEL = 23282.5783 RESTRAINT = 0.0000 ESURF = 180.1532 minimization completed, ENE= -.10625606E+05 RMS= 0.174396E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0795E+04 1.7159E+01 1.1477E+02 C 6229 BOND = 1405.4150 ANGLE = 3752.6340 DIHED = 5415.4595 VDWAALS = -3979.6287 EEL = -34898.9097 EGB = -7726.3521 1-4 VDW = 1804.6233 1-4 EEL = 23249.9268 RESTRAINT = 0.0000 ESURF = 181.4566 minimization completed, ENE= -.10795376E+05 RMS= 0.171590E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0573E+04 1.7375E+01 1.1567E+02 C 6166 BOND = 1388.5085 ANGLE = 3875.6794 DIHED = 5433.7526 VDWAALS = -3897.7125 EEL = -34977.4526 EGB = -7623.7637 1-4 VDW = 1836.3513 1-4 EEL = 23209.8608 RESTRAINT = 0.0000 ESURF = 181.4040 minimization completed, ENE= -.10573372E+05 RMS= 0.173755E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0710E+04 1.7087E+01 1.2851E+02 C 7490 BOND = 1408.8043 ANGLE = 3739.4821 DIHED = 5429.8100 VDWAALS = -3944.9946 EEL = -34925.3293 EGB = -7685.9136 1-4 VDW = 1806.5650 1-4 EEL = 23280.0144 RESTRAINT = 0.0000 ESURF = 181.7520 minimization completed, ENE= -.10709810E+05 RMS= 0.170871E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0743E+04 1.7158E+01 1.2217E+02 C 5249 BOND = 1420.2927 ANGLE = 3756.0467 DIHED = 5433.1153 VDWAALS = -3925.2516 EEL = -35090.3268 EGB = -7629.4181 1-4 VDW = 1787.8368 1-4 EEL = 23322.2011 RESTRAINT = 0.0000 ESURF = 182.7362 minimization completed, ENE= -.10742768E+05 RMS= 0.171576E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0795E+04 1.7156E+01 1.2751E+02 C 5728 BOND = 1405.5569 ANGLE = 3750.5578 DIHED = 5435.8929 VDWAALS = -3896.9034 EEL = -35125.3541 EGB = -7607.1388 1-4 VDW = 1808.5420 1-4 EEL = 23252.1342 RESTRAINT = 0.0000 ESURF = 181.9569 minimization completed, ENE= -.10794756E+05 RMS= 0.171564E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0720E+04 1.7521E+01 1.2099E+02 C 6239 BOND = 1468.8903 ANGLE = 3737.4556 DIHED = 5425.9336 VDWAALS = -3946.1955 EEL = -34984.2265 EGB = -7692.3571 1-4 VDW = 1774.6776 1-4 EEL = 23312.7485 RESTRAINT = 0.0000 ESURF = 182.7691 minimization completed, ENE= -.10720304E+05 RMS= 0.175214E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0659E+04 1.7422E+01 1.1401E+02 CA 6743 BOND = 1413.5984 ANGLE = 3776.2348 DIHED = 5446.1348 VDWAALS = -3932.0285 EEL = -35012.8349 EGB = -7597.3440 1-4 VDW = 1791.4842 1-4 EEL = 23274.1101 RESTRAINT = 0.0000 ESURF = 181.7820 minimization completed, ENE= -.10658863E+05 RMS= 0.174218E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0795E+04 1.7347E+01 1.0452E+02 C 6420 BOND = 1399.7667 ANGLE = 3793.0612 DIHED = 5431.4362 VDWAALS = -3954.7768 EEL = -35022.1955 EGB = -7681.4604 1-4 VDW = 1783.3279 1-4 EEL = 23274.2643 RESTRAINT = 0.0000 ESURF = 181.6518 minimization completed, ENE= -.10794925E+05 RMS= 0.173465E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0759E+04 1.7409E+01 1.3568E+02 CZ 862 BOND = 1401.4117 ANGLE = 3766.1296 DIHED = 5380.3407 VDWAALS = -3851.3620 EEL = -35073.3272 EGB = -7609.3487 1-4 VDW = 1794.7072 1-4 EEL = 23249.6722 RESTRAINT = 0.0000 ESURF = 183.1376 minimization completed, ENE= -.10758639E+05 RMS= 0.174087E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0690E+04 1.7227E+01 1.2539E+02 C 1959 BOND = 1425.5720 ANGLE = 3792.9857 DIHED = 5430.0780 VDWAALS = -3924.3444 EEL = -34930.4734 EGB = -7673.9801 1-4 VDW = 1763.1406 1-4 EEL = 23244.6756 RESTRAINT = 0.0000 ESURF = 182.0561 minimization completed, ENE= -.10690290E+05 RMS= 0.172266E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0767E+04 1.7196E+01 1.1901E+02 C 1502 BOND = 1397.9218 ANGLE = 3731.8748 DIHED = 5376.1969 VDWAALS = -3933.4212 EEL = -35186.4385 EGB = -7447.0091 1-4 VDW = 1809.1161 1-4 EEL = 23303.3559 RESTRAINT = 0.0000 ESURF = 181.0567 minimization completed, ENE= -.10767346E+05 RMS= 0.171965E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0824E+04 1.7005E+01 1.1834E+02 C 1852 BOND = 1457.7175 ANGLE = 3725.3546 DIHED = 5391.9754 VDWAALS = -3902.8568 EEL = -35136.0747 EGB = -7495.5471 1-4 VDW = 1744.0591 1-4 EEL = 23211.1691 RESTRAINT = 0.0000 ESURF = 180.6514 minimization completed, ENE= -.10823552E+05 RMS= 0.170052E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0754E+04 1.7208E+01 9.5099E+01 C 986 BOND = 1403.3193 ANGLE = 3726.9419 DIHED = 5390.2365 VDWAALS = -3921.9159 EEL = -34887.5290 EGB = -7715.9476 1-4 VDW = 1789.4846 1-4 EEL = 23279.4652 RESTRAINT = 0.0000 ESURF = 181.9189 minimization completed, ENE= -.10754026E+05 RMS= 0.172080E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0690E+04 1.7535E+01 1.1141E+02 C 1325 BOND = 1465.6153 ANGLE = 3748.1119 DIHED = 5438.9205 VDWAALS = -3943.5823 EEL = -35054.0058 EGB = -7563.7209 1-4 VDW = 1790.9726 1-4 EEL = 23249.3918 RESTRAINT = 0.0000 ESURF = 178.5697 minimization completed, ENE= -.10689727E+05 RMS= 0.175349E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0753E+04 1.7450E+01 1.2754E+02 C 1560 BOND = 1426.5335 ANGLE = 3745.9051 DIHED = 5397.7822 VDWAALS = -3875.2139 EEL = -35234.3691 EGB = -7505.4623 1-4 VDW = 1812.3720 1-4 EEL = 23300.5795 RESTRAINT = 0.0000 ESURF = 178.7866 minimization completed, ENE= -.10753086E+05 RMS= 0.174497E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0694E+04 1.7310E+01 1.0182E+02 N 3361 BOND = 1425.9062 ANGLE = 3774.6189 DIHED = 5426.8916 VDWAALS = -3902.4960 EEL = -35154.9563 EGB = -7602.7278 1-4 VDW = 1808.2870 1-4 EEL = 23351.2199 RESTRAINT = 0.0000 ESURF = 179.1636 minimization completed, ENE= -.10694093E+05 RMS= 0.173099E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0680E+04 1.7494E+01 1.1790E+02 C 4663 BOND = 1425.0313 ANGLE = 3840.3539 DIHED = 5419.3251 VDWAALS = -3952.3308 EEL = -35081.2924 EGB = -7555.8488 1-4 VDW = 1791.1578 1-4 EEL = 23255.6367 RESTRAINT = 0.0000 ESURF = 178.3859 minimization completed, ENE= -.10679581E+05 RMS= 0.174942E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 714.94 ( 7.74% of Gen B) | Calc gb diag 5433.00 (58.80% of Gen B) | Calc gb off-diag 3091.31 (33.46% of Gen B) | Gen Born time 9239.25 (100.0% of Nonbo) | Nonbond force 9239.25 (99.89% of Force) | Bond/Angle/Dihedral 9.93 ( 0.11% of Force) | Force time 9249.19 (100.0% of Runmd) | Runmd Time 9249.19 (99.02% of Total) | Other 91.12 ( 0.98% of Total) | Total time 9340.73 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 19:12:36.559 on 10/19/2010 | Setup done at 19:12:38.123 on 10/19/2010 | Run done at 21:48:17.289 on 10/19/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/19/2010 at 19:12:36 [-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 -1.0633E+04 1.7290E+01 1.2205E+02 CA 3676 BOND = 1394.6022 ANGLE = 3765.4446 DIHED = 5472.0314 VDWAALS = -3936.5246 EEL = -34981.2806 EGB = -7688.1408 1-4 VDW = 1836.4531 1-4 EEL = 23322.6662 RESTRAINT = 0.0000 ESURF = 181.4485 minimization completed, ENE= -.10633300E+05 RMS= 0.172900E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0613E+04 1.7433E+01 1.2278E+02 C 2233 BOND = 1415.5474 ANGLE = 3749.1646 DIHED = 5456.3123 VDWAALS = -3969.7422 EEL = -34857.1448 EGB = -7713.8678 1-4 VDW = 1801.7959 1-4 EEL = 23322.2988 RESTRAINT = 0.0000 ESURF = 183.0957 minimization completed, ENE= -.10612540E+05 RMS= 0.174331E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0778E+04 1.6998E+01 1.1925E+02 N 6931 BOND = 1360.4053 ANGLE = 3708.6660 DIHED = 5417.4583 VDWAALS = -3930.4260 EEL = -34930.6538 EGB = -7723.1975 1-4 VDW = 1833.1847 1-4 EEL = 23303.2089 RESTRAINT = 0.0000 ESURF = 183.5891 minimization completed, ENE= -.10777765E+05 RMS= 0.169977E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0697E+04 1.7654E+01 1.2749E+02 C 2886 BOND = 1432.7461 ANGLE = 3776.2491 DIHED = 5408.9059 VDWAALS = -3908.8392 EEL = -34923.4806 EGB = -7757.3725 1-4 VDW = 1807.6053 1-4 EEL = 23284.7567 RESTRAINT = 0.0000 ESURF = 182.5743 minimization completed, ENE= -.10696855E+05 RMS= 0.176541E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0740E+04 1.7171E+01 1.2313E+02 C 4018 BOND = 1401.3689 ANGLE = 3752.6616 DIHED = 5373.3235 VDWAALS = -3958.7702 EEL = -34842.7292 EGB = -7766.8660 1-4 VDW = 1801.0135 1-4 EEL = 23316.1423 RESTRAINT = 0.0000 ESURF = 183.3633 minimization completed, ENE= -.10740492E+05 RMS= 0.171713E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0667E+04 1.7546E+01 1.1204E+02 CD 2390 BOND = 1469.9380 ANGLE = 3758.6563 DIHED = 5387.2065 VDWAALS = -3925.6794 EEL = -34798.2774 EGB = -7839.5262 1-4 VDW = 1790.9063 1-4 EEL = 23309.1510 RESTRAINT = 0.0000 ESURF = 180.8464 minimization completed, ENE= -.10666779E+05 RMS= 0.175456E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0642E+04 1.7622E+01 1.1423E+02 C 6087 BOND = 1447.3518 ANGLE = 3799.7454 DIHED = 5421.6924 VDWAALS = -3931.3523 EEL = -35095.4823 EGB = -7489.8289 1-4 VDW = 1791.3003 1-4 EEL = 23232.8772 RESTRAINT = 0.0000 ESURF = 181.3892 minimization completed, ENE= -.10642307E+05 RMS= 0.176223E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0732E+04 1.7403E+01 1.0534E+02 CA 5253 BOND = 1486.0606 ANGLE = 3729.6895 DIHED = 5350.5101 VDWAALS = -3916.3958 EEL = -35068.1717 EGB = -7522.8378 1-4 VDW = 1804.5437 1-4 EEL = 23221.9004 RESTRAINT = 0.0000 ESURF = 182.9318 minimization completed, ENE= -.10731769E+05 RMS= 0.174029E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0708E+04 1.7234E+01 1.0077E+02 C 1596 BOND = 1426.5655 ANGLE = 3706.0541 DIHED = 5424.1895 VDWAALS = -3885.4456 EEL = -35088.8820 EGB = -7535.1125 1-4 VDW = 1800.9594 1-4 EEL = 23260.7374 RESTRAINT = 0.0000 ESURF = 183.0816 minimization completed, ENE= -.10707853E+05 RMS= 0.172336E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0715E+04 1.7261E+01 1.1291E+02 CD 4507 BOND = 1406.3637 ANGLE = 3748.7898 DIHED = 5431.5305 VDWAALS = -3924.6863 EEL = -34940.1626 EGB = -7698.1921 1-4 VDW = 1789.2573 1-4 EEL = 23289.5248 RESTRAINT = 0.0000 ESURF = 182.8930 minimization completed, ENE= -.10714682E+05 RMS= 0.172614E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0653E+04 1.7435E+01 1.1433E+02 C 2179 BOND = 1414.5697 ANGLE = 3799.6136 DIHED = 5421.7327 VDWAALS = -3901.4811 EEL = -34973.2741 EGB = -7632.8972 1-4 VDW = 1777.6069 1-4 EEL = 23257.6083 RESTRAINT = 0.0000 ESURF = 183.1084 minimization completed, ENE= -.10653413E+05 RMS= 0.174347E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0763E+04 1.7264E+01 1.0925E+02 CD 881 BOND = 1381.6134 ANGLE = 3760.2581 DIHED = 5410.3918 VDWAALS = -3883.6455 EEL = -35050.1281 EGB = -7623.2009 1-4 VDW = 1801.2824 1-4 EEL = 23258.5768 RESTRAINT = 0.0000 ESURF = 182.0978 minimization completed, ENE= -.10762754E+05 RMS= 0.172636E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0779E+04 1.7317E+01 1.2309E+02 C 7312 BOND = 1389.4285 ANGLE = 3721.5847 DIHED = 5414.5091 VDWAALS = -3880.9571 EEL = -35067.7207 EGB = -7621.6507 1-4 VDW = 1800.2861 1-4 EEL = 23285.1237 RESTRAINT = 0.0000 ESURF = 180.0293 minimization completed, ENE= -.10779367E+05 RMS= 0.173171E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0743E+04 1.7471E+01 1.0744E+02 CD 5431 BOND = 1448.5520 ANGLE = 3747.2092 DIHED = 5417.3681 VDWAALS = -3915.3010 EEL = -34950.5317 EGB = -7698.8170 1-4 VDW = 1771.4720 1-4 EEL = 23255.6413 RESTRAINT = 0.0000 ESURF = 181.5130 minimization completed, ENE= -.10742894E+05 RMS= 0.174708E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0671E+04 1.7549E+01 1.0575E+02 CA 6262 BOND = 1459.2134 ANGLE = 3790.0163 DIHED = 5398.8032 VDWAALS = -3911.6045 EEL = -34976.2250 EGB = -7709.0518 1-4 VDW = 1800.3271 1-4 EEL = 23296.6871 RESTRAINT = 0.0000 ESURF = 181.3312 minimization completed, ENE= -.10670503E+05 RMS= 0.175495E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0632E+04 1.7528E+01 1.1400E+02 C 3804 BOND = 1451.6833 ANGLE = 3780.3240 DIHED = 5419.5101 VDWAALS = -3891.9526 EEL = -35121.6613 EGB = -7565.4690 1-4 VDW = 1797.0345 1-4 EEL = 23317.3028 RESTRAINT = 0.0000 ESURF = 181.3802 minimization completed, ENE= -.10631848E+05 RMS= 0.175284E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0624E+04 1.7233E+01 1.1967E+02 C 2165 BOND = 1423.0910 ANGLE = 3809.8455 DIHED = 5440.7861 VDWAALS = -3872.1274 EEL = -35009.4726 EGB = -7638.1536 1-4 VDW = 1787.1053 1-4 EEL = 23256.1464 RESTRAINT = 0.0000 ESURF = 179.1979 minimization completed, ENE= -.10623581E+05 RMS= 0.172335E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0568E+04 1.7677E+01 1.0725E+02 CG 5371 BOND = 1492.5005 ANGLE = 3886.4048 DIHED = 5406.6362 VDWAALS = -3924.3046 EEL = -35021.9557 EGB = -7661.7663 1-4 VDW = 1791.6092 1-4 EEL = 23281.4799 RESTRAINT = 0.0000 ESURF = 181.7611 minimization completed, ENE= -.10567635E+05 RMS= 0.176768E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0717E+04 1.7413E+01 1.3310E+02 C 1978 BOND = 1392.3310 ANGLE = 3807.0455 DIHED = 5424.4865 VDWAALS = -3873.2018 EEL = -34984.3071 EGB = -7678.7534 1-4 VDW = 1774.1029 1-4 EEL = 23237.3828 RESTRAINT = 0.0000 ESURF = 184.1288 minimization completed, ENE= -.10716785E+05 RMS= 0.174128E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0738E+04 1.7305E+01 1.2032E+02 C 1978 BOND = 1400.1436 ANGLE = 3736.5128 DIHED = 5428.5484 VDWAALS = -3896.0345 EEL = -34907.7651 EGB = -7737.5974 1-4 VDW = 1791.9150 1-4 EEL = 23263.2653 RESTRAINT = 0.0000 ESURF = 183.4238 minimization completed, ENE= -.10737588E+05 RMS= 0.173053E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0597E+04 1.7374E+01 1.0671E+02 C 6206 BOND = 1419.8715 ANGLE = 3794.7870 DIHED = 5443.4369 VDWAALS = -3874.3726 EEL = -34944.7672 EGB = -7763.4797 1-4 VDW = 1818.2512 1-4 EEL = 23323.8012 RESTRAINT = 0.0000 ESURF = 185.1265 minimization completed, ENE= -.10597345E+05 RMS= 0.173743E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0727E+04 1.7309E+01 1.2486E+02 C 573 BOND = 1378.8355 ANGLE = 3748.6470 DIHED = 5408.5451 VDWAALS = -3849.3596 EEL = -34912.2458 EGB = -7809.9899 1-4 VDW = 1809.7145 1-4 EEL = 23313.4302 RESTRAINT = 0.0000 ESURF = 185.5576 minimization completed, ENE= -.10726865E+05 RMS= 0.173093E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0678E+04 1.7234E+01 1.0534E+02 C 7774 BOND = 1413.1210 ANGLE = 3766.4562 DIHED = 5411.7933 VDWAALS = -3938.2147 EEL = -34774.7906 EGB = -7770.2077 1-4 VDW = 1791.2768 1-4 EEL = 23237.6297 RESTRAINT = 0.0000 ESURF = 185.1884 minimization completed, ENE= -.10677747E+05 RMS= 0.172341E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0798E+04 1.7381E+01 1.2780E+02 C 4297 BOND = 1406.1476 ANGLE = 3739.1719 DIHED = 5409.3377 VDWAALS = -3935.4459 EEL = -34928.2956 EGB = -7782.4818 1-4 VDW = 1798.3842 1-4 EEL = 23310.6802 RESTRAINT = 0.0000 ESURF = 184.4858 minimization completed, ENE= -.10798016E+05 RMS= 0.173806E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0708E+04 1.7248E+01 1.2648E+02 C 4345 BOND = 1379.4153 ANGLE = 3778.0837 DIHED = 5379.4385 VDWAALS = -3838.9361 EEL = -35055.2027 EGB = -7681.8419 1-4 VDW = 1825.2675 1-4 EEL = 23321.3978 RESTRAINT = 0.0000 ESURF = 184.6937 minimization completed, ENE= -.10707684E+05 RMS= 0.172480E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0826E+04 1.7280E+01 1.1310E+02 C 5598 BOND = 1419.6857 ANGLE = 3716.6279 DIHED = 5434.2213 VDWAALS = -3891.6855 EEL = -34964.6027 EGB = -7781.0720 1-4 VDW = 1769.4822 1-4 EEL = 23287.0710 RESTRAINT = 0.0000 ESURF = 184.6970 minimization completed, ENE= -.10825575E+05 RMS= 0.172800E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0910E+04 1.7159E+01 1.2333E+02 C 4873 BOND = 1381.8280 ANGLE = 3686.6205 DIHED = 5363.3729 VDWAALS = -3912.1391 EEL = -35001.7342 EGB = -7742.0232 1-4 VDW = 1814.2157 1-4 EEL = 23316.7559 RESTRAINT = 0.0000 ESURF = 183.5854 minimization completed, ENE= -.10909518E+05 RMS= 0.171586E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0724E+04 1.7341E+01 1.2510E+02 N 7012 BOND = 1419.2322 ANGLE = 3745.8653 DIHED = 5424.1044 VDWAALS = -3897.5920 EEL = -34940.5741 EGB = -7741.2020 1-4 VDW = 1779.8951 1-4 EEL = 23302.8230 RESTRAINT = 0.0000 ESURF = 183.8140 minimization completed, ENE= -.10723634E+05 RMS= 0.173406E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0687E+04 1.7427E+01 9.6171E+01 C 4663 BOND = 1434.6622 ANGLE = 3737.3895 DIHED = 5441.7569 VDWAALS = -3948.5891 EEL = -34951.2578 EGB = -7767.8597 1-4 VDW = 1814.3047 1-4 EEL = 23370.1986 RESTRAINT = 0.0000 ESURF = 182.1636 minimization completed, ENE= -.10687231E+05 RMS= 0.174270E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0663E+04 1.7468E+01 1.2017E+02 C 3542 BOND = 1444.8924 ANGLE = 3739.1688 DIHED = 5421.1973 VDWAALS = -3864.1296 EEL = -34877.0838 EGB = -7789.3387 1-4 VDW = 1811.1549 1-4 EEL = 23270.3845 RESTRAINT = 0.0000 ESURF = 181.2002 minimization completed, ENE= -.10662554E+05 RMS= 0.174676E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0679E+04 1.7428E+01 1.0013E+02 C 5608 BOND = 1390.9043 ANGLE = 3726.9902 DIHED = 5426.6860 VDWAALS = -3914.1258 EEL = -34882.8279 EGB = -7809.5385 1-4 VDW = 1819.5220 1-4 EEL = 23380.5928 RESTRAINT = 0.0000 ESURF = 182.5630 minimization completed, ENE= -.10679234E+05 RMS= 0.174284E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0696E+04 1.7261E+01 1.1033E+02 CG 2253 BOND = 1421.1689 ANGLE = 3767.8808 DIHED = 5449.7830 VDWAALS = -3910.2488 EEL = -35017.9746 EGB = -7611.8279 1-4 VDW = 1809.1359 1-4 EEL = 23214.0329 RESTRAINT = 0.0000 ESURF = 181.6063 minimization completed, ENE= -.10696444E+05 RMS= 0.172608E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0792E+04 1.7186E+01 1.1247E+02 C 2806 BOND = 1401.2269 ANGLE = 3757.9000 DIHED = 5381.4639 VDWAALS = -3883.1372 EEL = -35024.7681 EGB = -7636.3587 1-4 VDW = 1766.8003 1-4 EEL = 23263.6891 RESTRAINT = 0.0000 ESURF = 181.6714 minimization completed, ENE= -.10791512E+05 RMS= 0.171856E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0755E+04 1.7294E+01 1.1232E+02 CD 3135 BOND = 1411.0733 ANGLE = 3736.2675 DIHED = 5456.7855 VDWAALS = -3913.2737 EEL = -35024.0100 EGB = -7687.1736 1-4 VDW = 1795.4687 1-4 EEL = 23287.9152 RESTRAINT = 0.0000 ESURF = 181.8242 minimization completed, ENE= -.10755123E+05 RMS= 0.172944E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0702E+04 1.7246E+01 1.2737E+02 C 773 BOND = 1390.7174 ANGLE = 3783.8450 DIHED = 5428.4529 VDWAALS = -3917.8341 EEL = -34897.6459 EGB = -7768.4482 1-4 VDW = 1805.5708 1-4 EEL = 23289.1079 RESTRAINT = 0.0000 ESURF = 184.0601 minimization completed, ENE= -.10702174E+05 RMS= 0.172457E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0759E+04 1.7446E+01 1.1646E+02 C 3578 BOND = 1437.7486 ANGLE = 3666.5531 DIHED = 5399.7098 VDWAALS = -3877.5479 EEL = -35014.3790 EGB = -7688.6876 1-4 VDW = 1810.3630 1-4 EEL = 23323.4607 RESTRAINT = 0.0000 ESURF = 183.3992 minimization completed, ENE= -.10759380E+05 RMS= 0.174460E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0632E+04 1.7475E+01 1.1008E+02 C 7625 BOND = 1438.0542 ANGLE = 3796.4170 DIHED = 5376.0483 VDWAALS = -3910.8561 EEL = -35083.2494 EGB = -7628.1763 1-4 VDW = 1852.5568 1-4 EEL = 23344.5338 RESTRAINT = 0.0000 ESURF = 182.1723 minimization completed, ENE= -.10632499E+05 RMS= 0.174745E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0693E+04 1.7616E+01 1.1798E+02 CG 1287 BOND = 1470.7662 ANGLE = 3811.0887 DIHED = 5421.4920 VDWAALS = -3902.5773 EEL = -35039.0104 EGB = -7744.5934 1-4 VDW = 1792.9629 1-4 EEL = 23315.3773 RESTRAINT = 0.0000 ESURF = 181.4637 minimization completed, ENE= -.10693030E+05 RMS= 0.176158E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0684E+04 1.7182E+01 1.2785E+02 C 278 BOND = 1385.0243 ANGLE = 3888.1305 DIHED = 5414.4583 VDWAALS = -3913.1423 EEL = -35061.5219 EGB = -7620.1795 1-4 VDW = 1764.3815 1-4 EEL = 23277.0615 RESTRAINT = 0.0000 ESURF = 181.6787 minimization completed, ENE= -.10684109E+05 RMS= 0.171816E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0738E+04 1.7300E+01 1.3231E+02 C 350 BOND = 1408.0458 ANGLE = 3812.8693 DIHED = 5403.8343 VDWAALS = -3890.3824 EEL = -35036.7281 EGB = -7700.3895 1-4 VDW = 1801.9309 1-4 EEL = 23280.4632 RESTRAINT = 0.0000 ESURF = 181.9621 minimization completed, ENE= -.10738395E+05 RMS= 0.172997E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0784E+04 1.7338E+01 1.2070E+02 C 7599 BOND = 1420.3051 ANGLE = 3713.7504 DIHED = 5349.3714 VDWAALS = -3916.8707 EEL = -34904.0196 EGB = -7774.6693 1-4 VDW = 1822.3361 1-4 EEL = 23325.0429 RESTRAINT = 0.0000 ESURF = 181.1596 minimization completed, ENE= -.10783594E+05 RMS= 0.173376E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0702E+04 1.7534E+01 1.5372E+02 C 845 BOND = 1438.5274 ANGLE = 3824.4623 DIHED = 5431.9547 VDWAALS = -3962.8808 EEL = -34917.5486 EGB = -7824.6236 1-4 VDW = 1817.6221 1-4 EEL = 23310.0063 RESTRAINT = 0.0000 ESURF = 180.1654 minimization completed, ENE= -.10702315E+05 RMS= 0.175337E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0798E+04 1.7472E+01 1.1486E+02 C 6229 BOND = 1477.9055 ANGLE = 3704.3210 DIHED = 5430.2718 VDWAALS = -3919.3297 EEL = -34834.0514 EGB = -7830.5042 1-4 VDW = 1771.1986 1-4 EEL = 23220.0731 RESTRAINT = 0.0000 ESURF = 182.1881 minimization completed, ENE= -.10797927E+05 RMS= 0.174723E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0777E+04 1.7375E+01 1.3347E+02 C 7095 BOND = 1440.0638 ANGLE = 3693.7726 DIHED = 5430.6528 VDWAALS = -3903.0653 EEL = -34861.1987 EGB = -7770.9289 1-4 VDW = 1771.8418 1-4 EEL = 23237.8061 RESTRAINT = 0.0000 ESURF = 183.7788 minimization completed, ENE= -.10777277E+05 RMS= 0.173748E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0790E+04 1.7355E+01 1.0623E+02 CA 7359 BOND = 1403.1857 ANGLE = 3695.4408 DIHED = 5413.7786 VDWAALS = -3923.0259 EEL = -34969.0833 EGB = -7767.3164 1-4 VDW = 1827.9850 1-4 EEL = 23346.7724 RESTRAINT = 0.0000 ESURF = 182.1387 minimization completed, ENE= -.10790124E+05 RMS= 0.173550E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0692E+04 1.7258E+01 1.2397E+02 C 5916 BOND = 1448.1928 ANGLE = 3692.6857 DIHED = 5451.0194 VDWAALS = -3901.0840 EEL = -34981.8553 EGB = -7648.7201 1-4 VDW = 1812.4319 1-4 EEL = 23251.6579 RESTRAINT = 0.0000 ESURF = 183.6998 minimization completed, ENE= -.10691972E+05 RMS= 0.172576E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0700E+04 1.7345E+01 1.1613E+02 N 514 BOND = 1420.3060 ANGLE = 3746.4499 DIHED = 5423.6880 VDWAALS = -3925.0219 EEL = -34823.0486 EGB = -7821.0104 1-4 VDW = 1789.6782 1-4 EEL = 23306.0257 RESTRAINT = 0.0000 ESURF = 182.6498 minimization completed, ENE= -.10700283E+05 RMS= 0.173446E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0638E+04 1.7698E+01 1.2460E+02 C 3858 BOND = 1504.2979 ANGLE = 3776.2819 DIHED = 5401.4288 VDWAALS = -3897.6003 EEL = -34914.0488 EGB = -7796.0717 1-4 VDW = 1812.4833 1-4 EEL = 23289.9163 RESTRAINT = 0.0000 ESURF = 185.4550 minimization completed, ENE= -.10637858E+05 RMS= 0.176979E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0721E+04 1.7245E+01 1.1225E+02 N 1071 BOND = 1393.3110 ANGLE = 3756.2337 DIHED = 5429.1609 VDWAALS = -3921.7665 EEL = -35071.5272 EGB = -7681.4071 1-4 VDW = 1805.6260 1-4 EEL = 23385.5495 RESTRAINT = 0.0000 ESURF = 184.0866 minimization completed, ENE= -.10720733E+05 RMS= 0.172449E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0780E+04 1.7156E+01 1.3812E+02 C 2030 BOND = 1393.8234 ANGLE = 3729.3087 DIHED = 5412.8436 VDWAALS = -3917.6712 EEL = -34856.8503 EGB = -7772.6550 1-4 VDW = 1785.0287 1-4 EEL = 23261.5940 RESTRAINT = 0.0000 ESURF = 184.3736 minimization completed, ENE= -.10780204E+05 RMS= 0.171562E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 712.72 ( 7.69% of Gen B) | Calc gb diag 5500.93 (59.36% of Gen B) | Calc gb off-diag 3052.74 (32.94% of Gen B) | Gen Born time 9266.40 (100.0% of Nonbo) | Nonbond force 9266.40 (100.0% of Force) | Bond/Angle/Dihedral 8.13 ( 0.09% of Force) | Force time 9274.54 (100.0% of Runmd) | Runmd Time 9274.54 (99.10% of Total) | Other 83.76 ( 0.90% of Total) | Total time 9358.35 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 19:12:36.559 on 10/19/2010 | Setup done at 19:12:37.121 on 10/19/2010 | Run done at 21:48:34.908 on 10/19/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/19/2010 at 19:12:36 [-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 -1.0688E+04 1.7478E+01 1.2542E+02 N 2737 BOND = 1426.2821 ANGLE = 3794.7832 DIHED = 5387.7706 VDWAALS = -3920.4541 EEL = -34908.7351 EGB = -7784.0702 1-4 VDW = 1796.1990 1-4 EEL = 23338.4915 RESTRAINT = 0.0000 ESURF = 181.4324 minimization completed, ENE= -.10688301E+05 RMS= 0.174782E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0818E+04 1.7241E+01 1.3161E+02 C 3459 BOND = 1385.6437 ANGLE = 3729.4341 DIHED = 5458.3502 VDWAALS = -3919.0994 EEL = -34849.0386 EGB = -7891.3065 1-4 VDW = 1772.3145 1-4 EEL = 23313.8549 RESTRAINT = 0.0000 ESURF = 181.7378 minimization completed, ENE= -.10818109E+05 RMS= 0.172410E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0757E+04 1.7153E+01 1.3141E+02 C 218 BOND = 1375.7251 ANGLE = 3834.3998 DIHED = 5436.5319 VDWAALS = -3950.7644 EEL = -35060.2452 EGB = -7667.6432 1-4 VDW = 1780.8811 1-4 EEL = 23312.6466 RESTRAINT = 0.0000 ESURF = 181.4665 minimization completed, ENE= -.10757002E+05 RMS= 0.171532E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0735E+04 1.7269E+01 1.4572E+02 CA 2847 BOND = 1390.9996 ANGLE = 3756.0894 DIHED = 5451.0687 VDWAALS = -3938.6951 EEL = -34963.2289 EGB = -7816.5602 1-4 VDW = 1823.5757 1-4 EEL = 23379.4902 RESTRAINT = 0.0000 ESURF = 181.8827 minimization completed, ENE= -.10735378E+05 RMS= 0.172687E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0692E+04 1.7560E+01 1.4210E+02 CD 2511 BOND = 1413.1947 ANGLE = 3814.2827 DIHED = 5454.6674 VDWAALS = -3914.0174 EEL = -35027.9984 EGB = -7744.3356 1-4 VDW = 1790.1135 1-4 EEL = 23339.7985 RESTRAINT = 0.0000 ESURF = 181.9506 minimization completed, ENE= -.10692344E+05 RMS= 0.175597E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0731E+04 1.7287E+01 1.2728E+02 C 4602 BOND = 1427.2395 ANGLE = 3792.6299 DIHED = 5444.5237 VDWAALS = -3902.2149 EEL = -35051.5879 EGB = -7743.1818 1-4 VDW = 1788.0819 1-4 EEL = 23327.8890 RESTRAINT = 0.0000 ESURF = 185.3541 minimization completed, ENE= -.10731266E+05 RMS= 0.172872E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0731E+04 1.7268E+01 1.5626E+02 CD 2390 BOND = 1401.4873 ANGLE = 3761.0020 DIHED = 5459.2600 VDWAALS = -3945.0453 EEL = -34900.0051 EGB = -7753.2284 1-4 VDW = 1798.3707 1-4 EEL = 23265.2486 RESTRAINT = 0.0000 ESURF = 181.7185 minimization completed, ENE= -.10731192E+05 RMS= 0.172678E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0794E+04 1.7519E+01 1.2231E+02 C 7062 BOND = 1455.7280 ANGLE = 3735.3062 DIHED = 5402.2254 VDWAALS = -3908.9165 EEL = -35108.5313 EGB = -7751.3611 1-4 VDW = 1795.6362 1-4 EEL = 23401.2885 RESTRAINT = 0.0000 ESURF = 185.0491 minimization completed, ENE= -.10793576E+05 RMS= 0.175192E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0777E+04 1.7009E+01 1.0431E+02 CA 1931 BOND = 1402.9205 ANGLE = 3732.5330 DIHED = 5428.1492 VDWAALS = -3917.1631 EEL = -35026.9238 EGB = -7642.8490 1-4 VDW = 1763.9038 1-4 EEL = 23298.4603 RESTRAINT = 0.0000 ESURF = 183.9997 minimization completed, ENE= -.10776969E+05 RMS= 0.170092E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0686E+04 1.7426E+01 1.2246E+02 C 7123 BOND = 1421.7512 ANGLE = 3767.3812 DIHED = 5421.9575 VDWAALS = -3894.9007 EEL = -35012.3198 EGB = -7734.0346 1-4 VDW = 1805.2351 1-4 EEL = 23357.5705 RESTRAINT = 0.0000 ESURF = 181.4246 minimization completed, ENE= -.10685935E+05 RMS= 0.174261E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0681E+04 1.7485E+01 1.0609E+02 CZ 6437 BOND = 1432.3413 ANGLE = 3799.2227 DIHED = 5450.4586 VDWAALS = -3964.1609 EEL = -35022.7966 EGB = -7670.0506 1-4 VDW = 1803.2867 1-4 EEL = 23309.2331 RESTRAINT = 0.0000 ESURF = 181.9368 minimization completed, ENE= -.10680529E+05 RMS= 0.174853E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0670E+04 1.7580E+01 1.2255E+02 CG 4868 BOND = 1442.1334 ANGLE = 3771.1070 DIHED = 5461.7479 VDWAALS = -3978.9195 EEL = -35083.8518 EGB = -7639.3411 1-4 VDW = 1789.1721 1-4 EEL = 23386.5490 RESTRAINT = 0.0000 ESURF = 181.3388 minimization completed, ENE= -.10670064E+05 RMS= 0.175804E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0620E+04 1.7553E+01 1.1310E+02 N 1504 BOND = 1444.5582 ANGLE = 3763.3561 DIHED = 5437.3552 VDWAALS = -4003.4437 EEL = -34931.9425 EGB = -7621.7799 1-4 VDW = 1810.9585 1-4 EEL = 23300.4995 RESTRAINT = 0.0000 ESURF = 180.7607 minimization completed, ENE= -.10619678E+05 RMS= 0.175526E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0618E+04 1.7438E+01 1.0912E+02 C 6509 BOND = 1363.9242 ANGLE = 3890.9559 DIHED = 5466.0972 VDWAALS = -3910.3513 EEL = -35140.5479 EGB = -7581.8588 1-4 VDW = 1826.6281 1-4 EEL = 23287.9021 RESTRAINT = 0.0000 ESURF = 179.6775 minimization completed, ENE= -.10617573E+05 RMS= 0.174377E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0620E+04 1.7593E+01 9.7158E+01 CB 4814 BOND = 1434.1940 ANGLE = 3794.6218 DIHED = 5416.2817 VDWAALS = -3909.8655 EEL = -35084.2783 EGB = -7649.2042 1-4 VDW = 1829.9143 1-4 EEL = 23366.9042 RESTRAINT = 0.0000 ESURF = 181.0288 minimization completed, ENE= -.10620403E+05 RMS= 0.175926E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0868E+04 1.7011E+01 1.1714E+02 C 6389 BOND = 1369.4264 ANGLE = 3778.5066 DIHED = 5427.5802 VDWAALS = -3953.2905 EEL = -35095.7192 EGB = -7626.1996 1-4 VDW = 1787.3981 1-4 EEL = 23263.5677 RESTRAINT = 0.0000 ESURF = 181.0098 minimization completed, ENE= -.10867720E+05 RMS= 0.170106E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0784E+04 1.7382E+01 1.1470E+02 N 2622 BOND = 1452.0259 ANGLE = 3747.5288 DIHED = 5410.9176 VDWAALS = -3943.6142 EEL = -35108.5535 EGB = -7541.3196 1-4 VDW = 1781.1397 1-4 EEL = 23238.2629 RESTRAINT = 0.0000 ESURF = 180.0901 minimization completed, ENE= -.10783522E+05 RMS= 0.173822E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0819E+04 1.7383E+01 1.0707E+02 C 5315 BOND = 1391.4811 ANGLE = 3703.0043 DIHED = 5418.8699 VDWAALS = -3882.2828 EEL = -35104.5232 EGB = -7624.7968 1-4 VDW = 1809.9981 1-4 EEL = 23286.3770 RESTRAINT = 0.0000 ESURF = 182.6546 minimization completed, ENE= -.10819218E+05 RMS= 0.173825E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0668E+04 1.7254E+01 1.0199E+02 N 2021 BOND = 1416.6110 ANGLE = 3794.1399 DIHED = 5453.7810 VDWAALS = -3932.5699 EEL = -35107.2621 EGB = -7565.3396 1-4 VDW = 1793.9644 1-4 EEL = 23297.7281 RESTRAINT = 0.0000 ESURF = 180.7640 minimization completed, ENE= -.10668183E+05 RMS= 0.172545E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0715E+04 1.7376E+01 1.1235E+02 N 1475 BOND = 1465.8633 ANGLE = 3777.3087 DIHED = 5385.0282 VDWAALS = -3942.2921 EEL = -35048.2641 EGB = -7686.6231 1-4 VDW = 1803.6380 1-4 EEL = 23347.2855 RESTRAINT = 0.0000 ESURF = 183.0820 minimization completed, ENE= -.10714974E+05 RMS= 0.173762E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0642E+04 1.7644E+01 1.2449E+02 CD 2268 BOND = 1425.5733 ANGLE = 3783.6898 DIHED = 5452.1558 VDWAALS = -3906.5440 EEL = -35156.2217 EGB = -7552.8130 1-4 VDW = 1843.2904 1-4 EEL = 23288.3188 RESTRAINT = 0.0000 ESURF = 181.0318 minimization completed, ENE= -.10641519E+05 RMS= 0.176441E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0703E+04 1.7320E+01 9.9780E+01 C 6683 BOND = 1415.2362 ANGLE = 3801.5101 DIHED = 5411.4534 VDWAALS = -3925.8135 EEL = -35172.5338 EGB = -7494.7377 1-4 VDW = 1808.7477 1-4 EEL = 23273.8731 RESTRAINT = 0.0000 ESURF = 178.8809 minimization completed, ENE= -.10703384E+05 RMS= 0.173200E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0750E+04 1.7308E+01 1.0209E+02 C 2972 BOND = 1410.0074 ANGLE = 3702.9484 DIHED = 5420.2502 VDWAALS = -3909.9503 EEL = -35092.7632 EGB = -7540.5860 1-4 VDW = 1818.4480 1-4 EEL = 23261.0162 RESTRAINT = 0.0000 ESURF = 180.7926 minimization completed, ENE= -.10749837E+05 RMS= 0.173079E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0833E+04 1.7078E+01 1.1801E+02 CZ 7137 BOND = 1317.7591 ANGLE = 3730.7295 DIHED = 5428.0595 VDWAALS = -3916.5895 EEL = -35224.8764 EGB = -7532.1055 1-4 VDW = 1821.5282 1-4 EEL = 23359.1982 RESTRAINT = 0.0000 ESURF = 182.8266 minimization completed, ENE= -.10833470E+05 RMS= 0.170779E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0774E+04 1.7156E+01 1.0905E+02 CG 1287 BOND = 1398.5829 ANGLE = 3691.3725 DIHED = 5412.1250 VDWAALS = -3899.7388 EEL = -35050.0628 EGB = -7561.2102 1-4 VDW = 1789.6006 1-4 EEL = 23264.7765 RESTRAINT = 0.0000 ESURF = 181.0408 minimization completed, ENE= -.10773514E+05 RMS= 0.171557E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0817E+04 1.7348E+01 1.2579E+02 CD2 7114 BOND = 1415.5783 ANGLE = 3730.5339 DIHED = 5374.7781 VDWAALS = -3955.9765 EEL = -34951.7209 EGB = -7679.8645 1-4 VDW = 1791.9037 1-4 EEL = 23277.7620 RESTRAINT = 0.0000 ESURF = 180.2715 minimization completed, ENE= -.10816734E+05 RMS= 0.173481E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0706E+04 1.7182E+01 1.2414E+02 C 4617 BOND = 1394.3386 ANGLE = 3838.8280 DIHED = 5427.3219 VDWAALS = -3910.8092 EEL = -35088.8406 EGB = -7655.3856 1-4 VDW = 1810.3667 1-4 EEL = 23296.7288 RESTRAINT = 0.0000 ESURF = 181.5396 minimization completed, ENE= -.10705912E+05 RMS= 0.171820E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0788E+04 1.7200E+01 1.1490E+02 CZ 4241 BOND = 1425.3560 ANGLE = 3740.2739 DIHED = 5404.4884 VDWAALS = -3931.1887 EEL = -34894.9358 EGB = -7756.3130 1-4 VDW = 1789.8858 1-4 EEL = 23254.1185 RESTRAINT = 0.0000 ESURF = 180.1529 minimization completed, ENE= -.10788162E+05 RMS= 0.172004E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0871E+04 1.7252E+01 1.0745E+02 C 1576 BOND = 1374.5270 ANGLE = 3689.2347 DIHED = 5413.6748 VDWAALS = -3937.3989 EEL = -35024.6980 EGB = -7672.7082 1-4 VDW = 1778.0386 1-4 EEL = 23328.3773 RESTRAINT = 0.0000 ESURF = 180.2043 minimization completed, ENE= -.10870748E+05 RMS= 0.172519E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0789E+04 1.7034E+01 1.1575E+02 N 3386 BOND = 1338.7004 ANGLE = 3749.1355 DIHED = 5448.1218 VDWAALS = -3922.6142 EEL = -34988.6215 EGB = -7706.5308 1-4 VDW = 1800.2017 1-4 EEL = 23311.5828 RESTRAINT = 0.0000 ESURF = 181.1829 minimization completed, ENE= -.10788841E+05 RMS= 0.170340E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0752E+04 1.7121E+01 1.2796E+02 C 4388 BOND = 1385.9112 ANGLE = 3720.4699 DIHED = 5404.5433 VDWAALS = -3886.3695 EEL = -35101.3304 EGB = -7555.9987 1-4 VDW = 1820.9915 1-4 EEL = 23278.6179 RESTRAINT = 0.0000 ESURF = 180.7484 minimization completed, ENE= -.10752416E+05 RMS= 0.171211E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0749E+04 1.7443E+01 1.1825E+02 C 3923 BOND = 1395.2027 ANGLE = 3724.2410 DIHED = 5407.1711 VDWAALS = -3931.3134 EEL = -35098.3329 EGB = -7649.7872 1-4 VDW = 1826.5006 1-4 EEL = 23394.3385 RESTRAINT = 0.0000 ESURF = 182.9408 minimization completed, ENE= -.10749039E+05 RMS= 0.174434E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0805E+04 1.7370E+01 1.2148E+02 C 5266 BOND = 1384.1400 ANGLE = 3675.1049 DIHED = 5420.3114 VDWAALS = -3946.7246 EEL = -34898.9452 EGB = -7743.0341 1-4 VDW = 1820.4440 1-4 EEL = 23301.5473 RESTRAINT = 0.0000 ESURF = 181.6726 minimization completed, ENE= -.10805484E+05 RMS= 0.173703E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0780E+04 1.7332E+01 1.2241E+02 C 2420 BOND = 1395.3289 ANGLE = 3707.0612 DIHED = 5377.7961 VDWAALS = -3907.0028 EEL = -35058.2035 EGB = -7707.5450 1-4 VDW = 1828.6129 1-4 EEL = 23401.9355 RESTRAINT = 0.0000 ESURF = 181.7783 minimization completed, ENE= -.10780238E+05 RMS= 0.173316E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0789E+04 1.7395E+01 9.9828E+01 C 1059 BOND = 1403.0081 ANGLE = 3683.2998 DIHED = 5402.5761 VDWAALS = -3931.4993 EEL = -34897.0220 EGB = -7731.8341 1-4 VDW = 1818.1056 1-4 EEL = 23284.4187 RESTRAINT = 0.0000 ESURF = 180.1001 minimization completed, ENE= -.10788847E+05 RMS= 0.173951E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0675E+04 1.7404E+01 1.1783E+02 C6 7863 BOND = 1398.7659 ANGLE = 3800.4892 DIHED = 5427.5172 VDWAALS = -3927.1758 EEL = -34934.8894 EGB = -7721.9921 1-4 VDW = 1798.1109 1-4 EEL = 23302.6290 RESTRAINT = 0.0000 ESURF = 181.1017 minimization completed, ENE= -.10675443E+05 RMS= 0.174040E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0802E+04 1.7236E+01 1.0950E+02 C 6192 BOND = 1442.9542 ANGLE = 3700.6998 DIHED = 5427.6323 VDWAALS = -3974.3273 EEL = -34922.4621 EGB = -7736.7473 1-4 VDW = 1787.9317 1-4 EEL = 23290.7723 RESTRAINT = 0.0000 ESURF = 181.2630 minimization completed, ENE= -.10802283E+05 RMS= 0.172361E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0711E+04 1.7195E+01 1.2103E+02 C 382 BOND = 1409.8604 ANGLE = 3793.1638 DIHED = 5442.3231 VDWAALS = -3950.6864 EEL = -34975.1522 EGB = -7711.6199 1-4 VDW = 1817.7455 1-4 EEL = 23280.5463 RESTRAINT = 0.0000 ESURF = 182.3445 minimization completed, ENE= -.10711475E+05 RMS= 0.171950E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0718E+04 1.7293E+01 1.0725E+02 N 3939 BOND = 1464.4953 ANGLE = 3750.3923 DIHED = 5411.6705 VDWAALS = -3930.2619 EEL = -35051.1794 EGB = -7670.8886 1-4 VDW = 1808.9108 1-4 EEL = 23317.6351 RESTRAINT = 0.0000 ESURF = 181.3926 minimization completed, ENE= -.10717833E+05 RMS= 0.172925E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0759E+04 1.7326E+01 1.1826E+02 C 2301 BOND = 1451.8039 ANGLE = 3686.3661 DIHED = 5401.9694 VDWAALS = -3947.9269 EEL = -34995.0293 EGB = -7603.2256 1-4 VDW = 1792.0283 1-4 EEL = 23274.3051 RESTRAINT = 0.0000 ESURF = 181.0127 minimization completed, ENE= -.10758696E+05 RMS= 0.173264E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0689E+04 1.7164E+01 1.0724E+02 N 4272 BOND = 1397.8796 ANGLE = 3786.6967 DIHED = 5447.1961 VDWAALS = -3928.5087 EEL = -34912.5333 EGB = -7756.8716 1-4 VDW = 1808.0968 1-4 EEL = 23286.5655 RESTRAINT = 0.0000 ESURF = 182.1622 minimization completed, ENE= -.10689317E+05 RMS= 0.171639E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0674E+04 1.7487E+01 1.0891E+02 CG 2732 BOND = 1391.2013 ANGLE = 3799.6066 DIHED = 5449.1550 VDWAALS = -3949.8733 EEL = -34992.4045 EGB = -7714.2417 1-4 VDW = 1813.6458 1-4 EEL = 23345.8094 RESTRAINT = 0.0000 ESURF = 183.5151 minimization completed, ENE= -.10673586E+05 RMS= 0.174870E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0694E+04 1.7361E+01 1.1037E+02 C 5189 BOND = 1421.7176 ANGLE = 3739.3933 DIHED = 5413.2976 VDWAALS = -3943.9052 EEL = -34820.7977 EGB = -7750.5853 1-4 VDW = 1802.3927 1-4 EEL = 23261.2551 RESTRAINT = 0.0000 ESURF = 183.1833 minimization completed, ENE= -.10694049E+05 RMS= 0.173614E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0672E+04 1.7579E+01 1.0810E+02 C 2660 BOND = 1484.0478 ANGLE = 3715.4673 DIHED = 5412.7857 VDWAALS = -3962.5305 EEL = -34824.9970 EGB = -7766.2866 1-4 VDW = 1816.2814 1-4 EEL = 23269.2159 RESTRAINT = 0.0000 ESURF = 184.0345 minimization completed, ENE= -.10671982E+05 RMS= 0.175787E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0706E+04 1.7468E+01 1.1962E+02 C 869 BOND = 1401.2619 ANGLE = 3772.8043 DIHED = 5432.9225 VDWAALS = -3939.2960 EEL = -34907.8735 EGB = -7756.4254 1-4 VDW = 1828.2588 1-4 EEL = 23279.3894 RESTRAINT = 0.0000 ESURF = 182.9986 minimization completed, ENE= -.10705959E+05 RMS= 0.174675E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0818E+04 1.7090E+01 1.0552E+02 C 608 BOND = 1352.7411 ANGLE = 3718.9260 DIHED = 5439.6003 VDWAALS = -3967.0536 EEL = -34752.7239 EGB = -7909.5233 1-4 VDW = 1804.2899 1-4 EEL = 23313.2344 RESTRAINT = 0.0000 ESURF = 182.6227 minimization completed, ENE= -.10817887E+05 RMS= 0.170900E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0646E+04 1.7307E+01 1.1315E+02 N 5397 BOND = 1406.0912 ANGLE = 3729.3285 DIHED = 5420.0741 VDWAALS = -3895.2570 EEL = -34797.8640 EGB = -7821.7318 1-4 VDW = 1828.0232 1-4 EEL = 23302.4984 RESTRAINT = 0.0000 ESURF = 182.6087 minimization completed, ENE= -.10646229E+05 RMS= 0.173068E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0754E+04 1.7200E+01 1.3125E+02 C 278 BOND = 1435.7320 ANGLE = 3741.1568 DIHED = 5405.7348 VDWAALS = -3927.3251 EEL = -34820.9927 EGB = -7850.2031 1-4 VDW = 1759.0736 1-4 EEL = 23320.0357 RESTRAINT = 0.0000 ESURF = 182.5828 minimization completed, ENE= -.10754205E+05 RMS= 0.172000E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0629E+04 1.7336E+01 1.0056E+02 C 71 BOND = 1425.5848 ANGLE = 3803.4102 DIHED = 5474.9593 VDWAALS = -3923.6338 EEL = -34857.9313 EGB = -7792.5654 1-4 VDW = 1817.5183 1-4 EEL = 23240.7863 RESTRAINT = 0.0000 ESURF = 182.8429 minimization completed, ENE= -.10629029E+05 RMS= 0.173364E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0738E+04 1.7476E+01 1.2988E+02 C 2233 BOND = 1465.8105 ANGLE = 3719.4459 DIHED = 5428.8205 VDWAALS = -3959.6364 EEL = -34828.9156 EGB = -7818.1264 1-4 VDW = 1776.2062 1-4 EEL = 23294.6305 RESTRAINT = 0.0000 ESURF = 183.2908 minimization completed, ENE= -.10738474E+05 RMS= 0.174758E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 701.76 ( 7.59% of Gen B) | Calc gb diag 5509.59 (59.56% of Gen B) | Calc gb off-diag 3039.12 (32.85% of Gen B) | Gen Born time 9250.48 (100.0% of Nonbo) | Nonbond force 9250.48 (100.0% of Force) | Bond/Angle/Dihedral 8.41 ( 0.09% of Force) | Force time 9258.90 (100.0% of Runmd) | Runmd Time 9258.90 (99.05% of Total) | Other 88.75 ( 0.95% of Total) | Total time 9347.68 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 19:12:36.557 on 10/19/2010 | Setup done at 19:12:37.235 on 10/19/2010 | Run done at 21:48:24.237 on 10/19/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/19/2010 at 19:12:36 [-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 -1.0731E+04 1.7229E+01 1.0728E+02 C 5098 BOND = 1412.9724 ANGLE = 3731.0739 DIHED = 5390.2433 VDWAALS = -3855.4510 EEL = -34738.1554 EGB = -7997.1499 1-4 VDW = 1821.7900 1-4 EEL = 23317.8131 RESTRAINT = 0.0000 ESURF = 186.0578 minimization completed, ENE= -.10730806E+05 RMS= 0.172294E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0806E+04 1.7213E+01 1.2332E+02 CZ 5225 BOND = 1410.1823 ANGLE = 3660.9568 DIHED = 5413.7150 VDWAALS = -3897.7543 EEL = -34694.9472 EGB = -7983.3392 1-4 VDW = 1798.0292 1-4 EEL = 23301.5964 RESTRAINT = 0.0000 ESURF = 185.9356 minimization completed, ENE= -.10805625E+05 RMS= 0.172129E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0623E+04 1.7367E+01 1.3861E+02 CD 1153 BOND = 1376.9446 ANGLE = 3850.2088 DIHED = 5412.9582 VDWAALS = -3931.6924 EEL = -34700.3310 EGB = -7949.4184 1-4 VDW = 1825.1377 1-4 EEL = 23308.7815 RESTRAINT = 0.0000 ESURF = 184.3260 minimization completed, ENE= -.10623085E+05 RMS= 0.173675E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0660E+04 1.7400E+01 1.1260E+02 C 2855 BOND = 1428.6219 ANGLE = 3701.8743 DIHED = 5426.1526 VDWAALS = -3922.6145 EEL = -34733.4747 EGB = -7908.8092 1-4 VDW = 1816.7235 1-4 EEL = 23348.0575 RESTRAINT = 0.0000 ESURF = 183.8443 minimization completed, ENE= -.10659624E+05 RMS= 0.173996E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0695E+04 1.7446E+01 1.0583E+02 C 6940 BOND = 1413.5579 ANGLE = 3787.8946 DIHED = 5411.4861 VDWAALS = -3937.6202 EEL = -34947.1598 EGB = -7822.0563 1-4 VDW = 1818.3463 1-4 EEL = 23397.6058 RESTRAINT = 0.0000 ESURF = 182.4983 minimization completed, ENE= -.10695447E+05 RMS= 0.174456E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0824E+04 1.7303E+01 1.0855E+02 C 436 BOND = 1427.1250 ANGLE = 3630.1702 DIHED = 5378.5045 VDWAALS = -3952.8060 EEL = -34893.2545 EGB = -7763.4165 1-4 VDW = 1824.5537 1-4 EEL = 23343.2974 RESTRAINT = 0.0000 ESURF = 181.4020 minimization completed, ENE= -.10824424E+05 RMS= 0.173032E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0627E+04 1.7626E+01 1.1484E+02 CD 881 BOND = 1466.6678 ANGLE = 3804.8887 DIHED = 5438.4765 VDWAALS = -3910.8156 EEL = -34841.2187 EGB = -7878.3371 1-4 VDW = 1810.1398 1-4 EEL = 23299.3346 RESTRAINT = 0.0000 ESURF = 183.4157 minimization completed, ENE= -.10627448E+05 RMS= 0.176260E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0702E+04 1.7260E+01 9.8104E+01 CA 4112 BOND = 1440.0153 ANGLE = 3797.4951 DIHED = 5418.5358 VDWAALS = -3947.4441 EEL = -34880.4071 EGB = -7741.6514 1-4 VDW = 1796.6354 1-4 EEL = 23234.7694 RESTRAINT = 0.0000 ESURF = 180.4499 minimization completed, ENE= -.10701602E+05 RMS= 0.172603E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0712E+04 1.7388E+01 1.1783E+02 C 4407 BOND = 1418.6714 ANGLE = 3820.8900 DIHED = 5420.4037 VDWAALS = -3976.2842 EEL = -34824.1979 EGB = -7826.4323 1-4 VDW = 1782.2626 1-4 EEL = 23291.6089 RESTRAINT = 0.0000 ESURF = 181.3389 minimization completed, ENE= -.10711739E+05 RMS= 0.173879E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0788E+04 1.7365E+01 1.0026E+02 C 2855 BOND = 1425.5218 ANGLE = 3740.3782 DIHED = 5396.4193 VDWAALS = -3886.4092 EEL = -34865.6306 EGB = -7794.0716 1-4 VDW = 1775.7235 1-4 EEL = 23237.3220 RESTRAINT = 0.0000 ESURF = 183.1060 minimization completed, ENE= -.10787641E+05 RMS= 0.173646E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0722E+04 1.7553E+01 1.1153E+02 N 6422 BOND = 1442.9492 ANGLE = 3739.3278 DIHED = 5432.2814 VDWAALS = -3986.6642 EEL = -34810.4287 EGB = -7895.5623 1-4 VDW = 1790.3715 1-4 EEL = 23383.7949 RESTRAINT = 0.0000 ESURF = 182.2871 minimization completed, ENE= -.10721643E+05 RMS= 0.175532E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0677E+04 1.7418E+01 1.0744E+02 N 122 BOND = 1475.6792 ANGLE = 3690.6927 DIHED = 5420.8732 VDWAALS = -3930.4319 EEL = -34869.9022 EGB = -7803.1954 1-4 VDW = 1823.0342 1-4 EEL = 23335.8975 RESTRAINT = 0.0000 ESURF = 180.4353 minimization completed, ENE= -.10676917E+05 RMS= 0.174179E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0720E+04 1.7456E+01 1.0307E+02 CA 2397 BOND = 1412.8356 ANGLE = 3778.1874 DIHED = 5428.0230 VDWAALS = -3932.7663 EEL = -34798.4383 EGB = -7873.7843 1-4 VDW = 1789.7925 1-4 EEL = 23294.1088 RESTRAINT = 0.0000 ESURF = 182.0212 minimization completed, ENE= -.10720020E+05 RMS= 0.174562E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0680E+04 1.7552E+01 1.0755E+02 CA 1176 BOND = 1452.1623 ANGLE = 3720.2199 DIHED = 5405.5040 VDWAALS = -3926.8323 EEL = -34881.5646 EGB = -7833.4026 1-4 VDW = 1808.3766 1-4 EEL = 23394.8976 RESTRAINT = 0.0000 ESURF = 180.8110 minimization completed, ENE= -.10679828E+05 RMS= 0.175521E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0753E+04 1.7138E+01 1.2761E+02 C 5748 BOND = 1398.2241 ANGLE = 3733.5206 DIHED = 5439.0277 VDWAALS = -3952.5538 EEL = -34766.5757 EGB = -7950.5597 1-4 VDW = 1820.8226 1-4 EEL = 23343.0505 RESTRAINT = 0.0000 ESURF = 181.6543 minimization completed, ENE= -.10753389E+05 RMS= 0.171382E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0836E+04 1.7343E+01 1.3899E+02 CG 4706 BOND = 1389.1941 ANGLE = 3658.4665 DIHED = 5375.6395 VDWAALS = -3986.6894 EEL = -34623.0586 EGB = -7930.3951 1-4 VDW = 1819.5736 1-4 EEL = 23278.6931 RESTRAINT = 0.0000 ESURF = 182.7256 minimization completed, ENE= -.10835851E+05 RMS= 0.173433E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0853E+04 1.7075E+01 1.3186E+02 C 2689 BOND = 1354.0708 ANGLE = 3664.4234 DIHED = 5452.5791 VDWAALS = -3964.8308 EEL = -34742.2057 EGB = -7882.4051 1-4 VDW = 1820.0995 1-4 EEL = 23264.3233 RESTRAINT = 0.0000 ESURF = 181.0722 minimization completed, ENE= -.10852873E+05 RMS= 0.170752E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0625E+04 1.7254E+01 1.2891E+02 C 5022 BOND = 1360.5846 ANGLE = 3771.1033 DIHED = 5450.1652 VDWAALS = -3916.4505 EEL = -34890.4331 EGB = -7818.0028 1-4 VDW = 1836.4713 1-4 EEL = 23399.5680 RESTRAINT = 0.0000 ESURF = 181.6639 minimization completed, ENE= -.10625330E+05 RMS= 0.172538E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0689E+04 1.7388E+01 1.2211E+02 C 6239 BOND = 1429.7100 ANGLE = 3758.9664 DIHED = 5452.5069 VDWAALS = -3952.4864 EEL = -34712.8391 EGB = -7897.7092 1-4 VDW = 1796.7793 1-4 EEL = 23252.8947 RESTRAINT = 0.0000 ESURF = 182.7549 minimization completed, ENE= -.10689422E+05 RMS= 0.173885E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0785E+04 1.7075E+01 1.2019E+02 CG 5359 BOND = 1365.4597 ANGLE = 3713.3079 DIHED = 5389.3358 VDWAALS = -3882.7219 EEL = -34814.7632 EGB = -7865.1884 1-4 VDW = 1827.0974 1-4 EEL = 23298.3472 RESTRAINT = 0.0000 ESURF = 183.9313 minimization completed, ENE= -.10785194E+05 RMS= 0.170751E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0820E+04 1.7262E+01 1.3466E+02 C 1349 BOND = 1387.2039 ANGLE = 3699.0359 DIHED = 5380.5780 VDWAALS = -3912.0243 EEL = -34743.7276 EGB = -7817.2788 1-4 VDW = 1801.2098 1-4 EEL = 23203.3569 RESTRAINT = 0.0000 ESURF = 181.9899 minimization completed, ENE= -.10819656E+05 RMS= 0.172621E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0727E+04 1.7443E+01 1.1443E+02 CB 6018 BOND = 1453.4304 ANGLE = 3703.1449 DIHED = 5403.8683 VDWAALS = -3953.7940 EEL = -34718.3618 EGB = -7896.4661 1-4 VDW = 1803.7853 1-4 EEL = 23294.6555 RESTRAINT = 0.0000 ESURF = 182.7530 minimization completed, ENE= -.10726985E+05 RMS= 0.174425E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0631E+04 1.7525E+01 1.4122E+02 C 2030 BOND = 1408.2695 ANGLE = 3814.5446 DIHED = 5491.0483 VDWAALS = -3940.9311 EEL = -34776.7775 EGB = -7806.4557 1-4 VDW = 1777.4693 1-4 EEL = 23218.4954 RESTRAINT = 0.0000 ESURF = 183.6732 minimization completed, ENE= -.10630664E+05 RMS= 0.175253E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0723E+04 1.7171E+01 1.1607E+02 C 1215 BOND = 1418.7808 ANGLE = 3766.1908 DIHED = 5400.7793 VDWAALS = -3939.8410 EEL = -34794.5344 EGB = -7817.9594 1-4 VDW = 1808.9948 1-4 EEL = 23251.5870 RESTRAINT = 0.0000 ESURF = 182.7622 minimization completed, ENE= -.10723240E+05 RMS= 0.171714E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0764E+04 1.7247E+01 1.0132E+02 C 3097 BOND = 1394.1829 ANGLE = 3774.0522 DIHED = 5410.5546 VDWAALS = -3946.1905 EEL = -34900.1172 EGB = -7754.1586 1-4 VDW = 1805.5295 1-4 EEL = 23270.3708 RESTRAINT = 0.0000 ESURF = 181.6760 minimization completed, ENE= -.10764100E+05 RMS= 0.172472E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0691E+04 1.7275E+01 1.1491E+02 C 3937 BOND = 1453.4618 ANGLE = 3752.1798 DIHED = 5425.8233 VDWAALS = -3974.5830 EEL = -34849.8816 EGB = -7707.1478 1-4 VDW = 1778.3512 1-4 EEL = 23249.6974 RESTRAINT = 0.0000 ESURF = 181.2089 minimization completed, ENE= -.10690890E+05 RMS= 0.172753E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0824E+04 1.7356E+01 1.1549E+02 C 450 BOND = 1428.1184 ANGLE = 3722.1150 DIHED = 5417.2867 VDWAALS = -3950.8693 EEL = -34818.1583 EGB = -7817.7368 1-4 VDW = 1787.4589 1-4 EEL = 23225.3553 RESTRAINT = 0.0000 ESURF = 182.5054 minimization completed, ENE= -.10823925E+05 RMS= 0.173560E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0721E+04 1.7286E+01 1.1632E+02 C 5044 BOND = 1407.2815 ANGLE = 3719.2056 DIHED = 5400.6933 VDWAALS = -3957.4723 EEL = -34739.3630 EGB = -7877.2291 1-4 VDW = 1834.1650 1-4 EEL = 23311.2368 RESTRAINT = 0.0000 ESURF = 180.9358 minimization completed, ENE= -.10720546E+05 RMS= 0.172859E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0744E+04 1.7148E+01 1.2015E+02 C 7116 BOND = 1383.0450 ANGLE = 3694.1941 DIHED = 5425.2191 VDWAALS = -3925.5336 EEL = -34829.9118 EGB = -7833.1789 1-4 VDW = 1820.5273 1-4 EEL = 23337.1855 RESTRAINT = 0.0000 ESURF = 184.4649 minimization completed, ENE= -.10743988E+05 RMS= 0.171477E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0745E+04 1.7373E+01 1.0502E+02 N 7083 BOND = 1418.7994 ANGLE = 3726.9964 DIHED = 5420.0579 VDWAALS = -3860.3903 EEL = -34913.6247 EGB = -7856.6460 1-4 VDW = 1807.9759 1-4 EEL = 23326.9873 RESTRAINT = 0.0000 ESURF = 184.3613 minimization completed, ENE= -.10745483E+05 RMS= 0.173728E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0788E+04 1.7154E+01 1.0708E+02 CG 961 BOND = 1417.2599 ANGLE = 3685.4462 DIHED = 5453.2352 VDWAALS = -3930.7305 EEL = -34835.4319 EGB = -7855.3631 1-4 VDW = 1805.9740 1-4 EEL = 23288.3211 RESTRAINT = 0.0000 ESURF = 183.6538 minimization completed, ENE= -.10787635E+05 RMS= 0.171539E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0754E+04 1.7091E+01 1.1112E+02 C 2751 BOND = 1418.4426 ANGLE = 3710.4430 DIHED = 5448.8967 VDWAALS = -3953.5074 EEL = -34748.6752 EGB = -7871.6884 1-4 VDW = 1770.2716 1-4 EEL = 23290.3933 RESTRAINT = 0.0000 ESURF = 181.5640 minimization completed, ENE= -.10753860E+05 RMS= 0.170909E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0828E+04 1.7157E+01 1.1581E+02 C 7055 BOND = 1377.5511 ANGLE = 3659.3737 DIHED = 5434.1642 VDWAALS = -3919.1975 EEL = -34879.4229 EGB = -7820.9610 1-4 VDW = 1813.2755 1-4 EEL = 23324.4094 RESTRAINT = 0.0000 ESURF = 182.7565 minimization completed, ENE= -.10828051E+05 RMS= 0.171567E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0734E+04 1.7246E+01 1.0810E+02 CD 5312 BOND = 1389.0148 ANGLE = 3775.4208 DIHED = 5409.4073 VDWAALS = -3978.3426 EEL = -34780.8052 EGB = -7803.0898 1-4 VDW = 1774.5968 1-4 EEL = 23297.8328 RESTRAINT = 0.0000 ESURF = 181.7310 minimization completed, ENE= -.10734234E+05 RMS= 0.172462E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0650E+04 1.7445E+01 1.0043E+02 CB 3864 BOND = 1462.8712 ANGLE = 3786.3395 DIHED = 5467.7859 VDWAALS = -3960.4775 EEL = -34929.3663 EGB = -7744.5541 1-4 VDW = 1796.9340 1-4 EEL = 23288.6884 RESTRAINT = 0.0000 ESURF = 181.9871 minimization completed, ENE= -.10649792E+05 RMS= 0.174445E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0767E+04 1.7291E+01 1.2297E+02 N 5849 BOND = 1397.0530 ANGLE = 3752.9843 DIHED = 5415.2654 VDWAALS = -3939.0298 EEL = -34887.4095 EGB = -7825.3529 1-4 VDW = 1787.3810 1-4 EEL = 23348.6988 RESTRAINT = 0.0000 ESURF = 183.4023 minimization completed, ENE= -.10767008E+05 RMS= 0.172914E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0816E+04 1.7310E+01 1.1038E+02 CD 3073 BOND = 1425.9306 ANGLE = 3737.5755 DIHED = 5386.9717 VDWAALS = -3968.8962 EEL = -34875.4130 EGB = -7782.9465 1-4 VDW = 1780.7042 1-4 EEL = 23296.5128 RESTRAINT = 0.0000 ESURF = 183.1421 minimization completed, ENE= -.10816419E+05 RMS= 0.173103E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0646E+04 1.7266E+01 1.2676E+02 CG 1629 BOND = 1387.9478 ANGLE = 3840.8729 DIHED = 5417.3296 VDWAALS = -3912.3501 EEL = -35007.7232 EGB = -7639.3985 1-4 VDW = 1783.8459 1-4 EEL = 23300.9070 RESTRAINT = 0.0000 ESURF = 182.6474 minimization completed, ENE= -.10645921E+05 RMS= 0.172664E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0795E+04 1.7056E+01 1.1155E+02 CD 5110 BOND = 1371.4564 ANGLE = 3725.3118 DIHED = 5411.1030 VDWAALS = -3913.2733 EEL = -34876.1330 EGB = -7823.8877 1-4 VDW = 1796.6304 1-4 EEL = 23330.5491 RESTRAINT = 0.0000 ESURF = 183.1548 minimization completed, ENE= -.10795089E+05 RMS= 0.170559E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0787E+04 1.7027E+01 1.1248E+02 CA 2996 BOND = 1384.1603 ANGLE = 3715.9056 DIHED = 5439.8604 VDWAALS = -3906.2491 EEL = -34732.3008 EGB = -7929.8075 1-4 VDW = 1799.6002 1-4 EEL = 23257.7413 RESTRAINT = 0.0000 ESURF = 184.2098 minimization completed, ENE= -.10786880E+05 RMS= 0.170266E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0759E+04 1.7147E+01 1.0085E+02 NE 534 BOND = 1399.8833 ANGLE = 3727.2070 DIHED = 5405.9270 VDWAALS = -3911.2851 EEL = -34775.6346 EGB = -7930.6156 1-4 VDW = 1790.1549 1-4 EEL = 23351.6757 RESTRAINT = 0.0000 ESURF = 183.4174 minimization completed, ENE= -.10759270E+05 RMS= 0.171473E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0761E+04 1.7351E+01 1.1955E+02 C 2432 BOND = 1429.8334 ANGLE = 3665.7282 DIHED = 5415.9431 VDWAALS = -3936.8221 EEL = -34923.0194 EGB = -7790.2749 1-4 VDW = 1827.6899 1-4 EEL = 23367.7476 RESTRAINT = 0.0000 ESURF = 182.3974 minimization completed, ENE= -.10760777E+05 RMS= 0.173513E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0773E+04 1.7291E+01 1.2043E+02 C 3090 BOND = 1411.7361 ANGLE = 3748.4105 DIHED = 5381.3790 VDWAALS = -3944.0425 EEL = -34976.2717 EGB = -7722.4670 1-4 VDW = 1800.7586 1-4 EEL = 23345.5287 RESTRAINT = 0.0000 ESURF = 182.1466 minimization completed, ENE= -.10772822E+05 RMS= 0.172913E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0766E+04 1.7324E+01 1.1780E+02 C 3951 BOND = 1408.9723 ANGLE = 3726.4358 DIHED = 5415.5842 VDWAALS = -3943.9786 EEL = -35046.7472 EGB = -7666.4530 1-4 VDW = 1796.4485 1-4 EEL = 23361.6593 RESTRAINT = 0.0000 ESURF = 181.7251 minimization completed, ENE= -.10766354E+05 RMS= 0.173240E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0820E+04 1.7251E+01 1.1172E+02 C 4188 BOND = 1354.7323 ANGLE = 3711.6731 DIHED = 5449.2552 VDWAALS = -3949.0971 EEL = -34959.3644 EGB = -7723.9942 1-4 VDW = 1779.8894 1-4 EEL = 23334.9971 RESTRAINT = 0.0000 ESURF = 182.2622 minimization completed, ENE= -.10819646E+05 RMS= 0.172513E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0795E+04 1.7124E+01 1.0742E+02 C 845 BOND = 1386.6897 ANGLE = 3775.6752 DIHED = 5382.7796 VDWAALS = -3919.3871 EEL = -34857.1479 EGB = -7767.8172 1-4 VDW = 1796.4275 1-4 EEL = 23224.9123 RESTRAINT = 0.0000 ESURF = 183.0279 minimization completed, ENE= -.10794840E+05 RMS= 0.171235E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0739E+04 1.7303E+01 1.3288E+02 C 6277 BOND = 1448.1027 ANGLE = 3722.5805 DIHED = 5429.3268 VDWAALS = -3922.2674 EEL = -35018.1355 EGB = -7682.9706 1-4 VDW = 1800.7643 1-4 EEL = 23300.7508 RESTRAINT = 0.0000 ESURF = 182.4906 minimization completed, ENE= -.10739358E+05 RMS= 0.173027E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0784E+04 1.7378E+01 1.2481E+02 CG 369 BOND = 1418.8561 ANGLE = 3747.2980 DIHED = 5451.7742 VDWAALS = -3927.0842 EEL = -35025.5271 EGB = -7705.3852 1-4 VDW = 1781.5992 1-4 EEL = 23294.8553 RESTRAINT = 0.0000 ESURF = 179.1923 minimization completed, ENE= -.10784421E+05 RMS= 0.173783E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0737E+04 1.7078E+01 1.0002E+02 C 6029 BOND = 1393.8959 ANGLE = 3780.1720 DIHED = 5451.3164 VDWAALS = -3942.9068 EEL = -34940.3262 EGB = -7738.4214 1-4 VDW = 1778.9258 1-4 EEL = 23300.1207 RESTRAINT = 0.0000 ESURF = 180.5884 minimization completed, ENE= -.10736635E+05 RMS= 0.170784E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0724E+04 1.7324E+01 1.3497E+02 C 1408 BOND = 1415.4322 ANGLE = 3735.2942 DIHED = 5425.6438 VDWAALS = -3944.3395 EEL = -34803.3017 EGB = -7872.5398 1-4 VDW = 1827.8842 1-4 EEL = 23310.3417 RESTRAINT = 0.0000 ESURF = 181.7469 minimization completed, ENE= -.10723838E+05 RMS= 0.173245E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 708.36 ( 7.70% of Gen B) | Calc gb diag 5439.55 (59.10% of Gen B) | Calc gb off-diag 3055.81 (33.20% of Gen B) | Gen Born time 9203.72 (100.0% of Nonbo) | Nonbond force 9203.72 (100.0% of Force) | Bond/Angle/Dihedral 8.86 ( 0.10% of Force) | Force time 9212.59 (100.0% of Runmd) | Runmd Time 9212.59 (99.16% of Total) | Other 78.24 ( 0.84% of Total) | Total time 9290.85 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 19:12:36.791 on 10/19/2010 | Setup done at 19:12:39.147 on 10/19/2010 | Run done at 21:47:27.640 on 10/19/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/19/2010 at 19:12:36 [-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 -1.0682E+04 1.7326E+01 1.3732E+02 C 5983 BOND = 1399.0293 ANGLE = 3758.1574 DIHED = 5422.0549 VDWAALS = -3876.0953 EEL = -35095.2028 EGB = -7685.1990 1-4 VDW = 1798.8897 1-4 EEL = 23411.4744 RESTRAINT = 0.0000 ESURF = 184.5586 minimization completed, ENE= -.10682333E+05 RMS= 0.173256E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0722E+04 1.7779E+01 1.2738E+02 N 7402 BOND = 1456.6379 ANGLE = 3696.8740 DIHED = 5448.1360 VDWAALS = -3957.8293 EEL = -34962.1847 EGB = -7812.6643 1-4 VDW = 1807.4212 1-4 EEL = 23418.1794 RESTRAINT = 0.0000 ESURF = 183.5713 minimization completed, ENE= -.10721859E+05 RMS= 0.177792E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0700E+04 1.7340E+01 1.1693E+02 N 7376 BOND = 1418.3087 ANGLE = 3702.4404 DIHED = 5473.5266 VDWAALS = -3869.8974 EEL = -34831.2827 EGB = -7935.5372 1-4 VDW = 1815.6626 1-4 EEL = 23341.0197 RESTRAINT = 0.0000 ESURF = 185.6624 minimization completed, ENE= -.10700097E+05 RMS= 0.173399E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0805E+04 1.7341E+01 1.0121E+02 CZ 5376 BOND = 1453.8683 ANGLE = 3665.0418 DIHED = 5389.1908 VDWAALS = -3925.7918 EEL = -34929.8616 EGB = -7774.3421 1-4 VDW = 1812.7608 1-4 EEL = 23320.6898 RESTRAINT = 0.0000 ESURF = 183.0139 minimization completed, ENE= -.10805430E+05 RMS= 0.173413E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0670E+04 1.7612E+01 1.2103E+02 C5 7862 BOND = 1434.3909 ANGLE = 3772.9339 DIHED = 5405.5505 VDWAALS = -3895.5653 EEL = -34944.6723 EGB = -7758.7827 1-4 VDW = 1795.3958 1-4 EEL = 23334.2107 RESTRAINT = 0.0000 ESURF = 186.4444 minimization completed, ENE= -.10670094E+05 RMS= 0.176117E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0667E+04 1.7373E+01 1.2179E+02 C 519 BOND = 1440.8570 ANGLE = 3753.5720 DIHED = 5434.0367 VDWAALS = -3897.8951 EEL = -34764.9857 EGB = -7951.4481 1-4 VDW = 1797.3708 1-4 EEL = 23333.1548 RESTRAINT = 0.0000 ESURF = 188.3679 minimization completed, ENE= -.10666970E+05 RMS= 0.173726E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0712E+04 1.7319E+01 9.8256E+01 C 1780 BOND = 1411.6261 ANGLE = 3721.8601 DIHED = 5390.2839 VDWAALS = -3932.9297 EEL = -34669.9141 EGB = -7969.5548 1-4 VDW = 1812.9039 1-4 EEL = 23337.2947 RESTRAINT = 0.0000 ESURF = 186.0243 minimization completed, ENE= -.10712406E+05 RMS= 0.173190E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0773E+04 1.7307E+01 1.2415E+02 C 673 BOND = 1462.1232 ANGLE = 3706.1625 DIHED = 5369.9920 VDWAALS = -3908.6752 EEL = -34628.0167 EGB = -8033.9100 1-4 VDW = 1789.1283 1-4 EEL = 23284.3119 RESTRAINT = 0.0000 ESURF = 185.9273 minimization completed, ENE= -.10772957E+05 RMS= 0.173071E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0764E+04 1.7222E+01 1.3339E+02 CD 4694 BOND = 1403.0719 ANGLE = 3745.0374 DIHED = 5432.3349 VDWAALS = -3901.9918 EEL = -34734.6037 EGB = -7990.4721 1-4 VDW = 1786.1130 1-4 EEL = 23310.1535 RESTRAINT = 0.0000 ESURF = 186.7084 minimization completed, ENE= -.10763648E+05 RMS= 0.172220E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0737E+04 1.7484E+01 1.3016E+02 CA 5 BOND = 1422.2069 ANGLE = 3758.7585 DIHED = 5421.1072 VDWAALS = -3922.0331 EEL = -34677.7232 EGB = -7952.0438 1-4 VDW = 1791.4030 1-4 EEL = 23235.4075 RESTRAINT = 0.0000 ESURF = 186.0848 minimization completed, ENE= -.10736832E+05 RMS= 0.174843E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0847E+04 1.7121E+01 1.1042E+02 C 7774 BOND = 1390.8460 ANGLE = 3606.8270 DIHED = 5415.7770 VDWAALS = -3904.3561 EEL = -34993.8190 EGB = -7786.4766 1-4 VDW = 1848.8287 1-4 EEL = 23388.4647 RESTRAINT = 0.0000 ESURF = 186.4959 minimization completed, ENE= -.10847412E+05 RMS= 0.171209E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0650E+04 1.7762E+01 1.0485E+02 C 4921 BOND = 1482.6576 ANGLE = 3740.1699 DIHED = 5446.0106 VDWAALS = -3865.1784 EEL = -34823.9588 EGB = -7876.3156 1-4 VDW = 1821.5135 1-4 EEL = 23237.0130 RESTRAINT = 0.0000 ESURF = 188.1175 minimization completed, ENE= -.10649971E+05 RMS= 0.177616E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0788E+04 1.7396E+01 1.1882E+02 N 3320 BOND = 1403.1337 ANGLE = 3707.9573 DIHED = 5390.1780 VDWAALS = -3887.2079 EEL = -34768.5507 EGB = -7850.2716 1-4 VDW = 1794.8589 1-4 EEL = 23234.6208 RESTRAINT = 0.0000 ESURF = 186.9887 minimization completed, ENE= -.10788293E+05 RMS= 0.173961E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0884E+04 1.7062E+01 1.1666E+02 CG 2610 BOND = 1370.5612 ANGLE = 3663.5380 DIHED = 5396.0333 VDWAALS = -3913.5456 EEL = -34896.6291 EGB = -7816.3656 1-4 VDW = 1801.9125 1-4 EEL = 23326.3589 RESTRAINT = 0.0000 ESURF = 184.0677 minimization completed, ENE= -.10884069E+05 RMS= 0.170620E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0753E+04 1.7112E+01 1.1061E+02 CA 1383 BOND = 1376.6739 ANGLE = 3728.3252 DIHED = 5422.5543 VDWAALS = -3923.0128 EEL = -34781.9038 EGB = -7976.3605 1-4 VDW = 1801.7331 1-4 EEL = 23413.7845 RESTRAINT = 0.0000 ESURF = 185.1238 minimization completed, ENE= -.10753082E+05 RMS= 0.171122E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0718E+04 1.7292E+01 1.0216E+02 N 2808 BOND = 1414.3177 ANGLE = 3736.5838 DIHED = 5449.4358 VDWAALS = -3905.3777 EEL = -34875.8870 EGB = -7774.7747 1-4 VDW = 1782.8051 1-4 EEL = 23269.9881 RESTRAINT = 0.0000 ESURF = 185.0265 minimization completed, ENE= -.10717882E+05 RMS= 0.172924E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0747E+04 1.7327E+01 1.1643E+02 CA 5387 BOND = 1446.6066 ANGLE = 3758.1282 DIHED = 5378.9768 VDWAALS = -3923.6472 EEL = -34842.4576 EGB = -7870.9840 1-4 VDW = 1803.0762 1-4 EEL = 23316.7084 RESTRAINT = 0.0000 ESURF = 187.0541 minimization completed, ENE= -.10746538E+05 RMS= 0.173274E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0701E+04 1.7573E+01 1.2758E+02 C 6799 BOND = 1424.9635 ANGLE = 3792.4993 DIHED = 5393.1393 VDWAALS = -3940.8629 EEL = -34735.7561 EGB = -7986.5514 1-4 VDW = 1818.3165 1-4 EEL = 23348.9308 RESTRAINT = 0.0000 ESURF = 184.3669 minimization completed, ENE= -.10700954E+05 RMS= 0.175728E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0796E+04 1.7405E+01 1.1472E+02 CG 7132 BOND = 1422.0381 ANGLE = 3688.5562 DIHED = 5409.3154 VDWAALS = -3980.9237 EEL = -34729.6635 EGB = -7873.7351 1-4 VDW = 1809.5710 1-4 EEL = 23278.2299 RESTRAINT = 0.0000 ESURF = 180.4695 minimization completed, ENE= -.10796142E+05 RMS= 0.174054E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0737E+04 1.7606E+01 1.1990E+02 NZ 3596 BOND = 1470.2850 ANGLE = 3729.0577 DIHED = 5443.5820 VDWAALS = -3931.7249 EEL = -35096.6802 EGB = -7599.4701 1-4 VDW = 1790.8846 1-4 EEL = 23276.8693 RESTRAINT = 0.0000 ESURF = 180.2656 minimization completed, ENE= -.10736931E+05 RMS= 0.176060E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0727E+04 1.7222E+01 1.2033E+02 CA 7655 BOND = 1436.2034 ANGLE = 3772.7138 DIHED = 5462.8418 VDWAALS = -3875.4627 EEL = -35071.4059 EGB = -7657.9508 1-4 VDW = 1765.4279 1-4 EEL = 23256.4100 RESTRAINT = 0.0000 ESURF = 184.3996 minimization completed, ENE= -.10726823E+05 RMS= 0.172220E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0735E+04 1.7298E+01 1.1455E+02 C 1677 BOND = 1411.4374 ANGLE = 3771.2160 DIHED = 5445.1040 VDWAALS = -3912.2986 EEL = -34795.1121 EGB = -7959.5308 1-4 VDW = 1802.1592 1-4 EEL = 23318.4250 RESTRAINT = 0.0000 ESURF = 183.5903 minimization completed, ENE= -.10735010E+05 RMS= 0.172980E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0786E+04 1.7170E+01 1.2489E+02 C 1550 BOND = 1350.6634 ANGLE = 3708.7254 DIHED = 5438.8584 VDWAALS = -3939.0251 EEL = -34713.2022 EGB = -7953.9920 1-4 VDW = 1799.4058 1-4 EEL = 23339.1397 RESTRAINT = 0.0000 ESURF = 183.9210 minimization completed, ENE= -.10785506E+05 RMS= 0.171702E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0638E+04 1.7303E+01 1.1244E+02 C 21 BOND = 1428.4469 ANGLE = 3750.3285 DIHED = 5430.1455 VDWAALS = -3900.5491 EEL = -34832.0283 EGB = -7842.5484 1-4 VDW = 1825.3155 1-4 EEL = 23316.7819 RESTRAINT = 0.0000 ESURF = 185.7602 minimization completed, ENE= -.10638347E+05 RMS= 0.173033E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0671E+04 1.7422E+01 1.1960E+02 C 5285 BOND = 1436.8183 ANGLE = 3729.6702 DIHED = 5406.5125 VDWAALS = -3903.8079 EEL = -34771.7507 EGB = -7952.0703 1-4 VDW = 1840.4855 1-4 EEL = 23357.4343 RESTRAINT = 0.0000 ESURF = 186.1499 minimization completed, ENE= -.10670558E+05 RMS= 0.174217E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0666E+04 1.7583E+01 1.1718E+02 C 3552 BOND = 1455.7553 ANGLE = 3761.8388 DIHED = 5412.1258 VDWAALS = -3912.0699 EEL = -34697.8352 EGB = -7940.7398 1-4 VDW = 1787.9269 1-4 EEL = 23282.1091 RESTRAINT = 0.0000 ESURF = 184.3898 minimization completed, ENE= -.10666499E+05 RMS= 0.175829E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0714E+04 1.7308E+01 1.0984E+02 C 5189 BOND = 1399.1762 ANGLE = 3750.2108 DIHED = 5429.4484 VDWAALS = -3893.0210 EEL = -34822.5364 EGB = -7889.8385 1-4 VDW = 1788.3437 1-4 EEL = 23338.5528 RESTRAINT = 0.0000 ESURF = 185.9776 minimization completed, ENE= -.10713687E+05 RMS= 0.173079E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0796E+04 1.7201E+01 9.9485E+01 C 6360 BOND = 1402.7830 ANGLE = 3735.7740 DIHED = 5392.2912 VDWAALS = -3912.8850 EEL = -34973.0142 EGB = -7744.4206 1-4 VDW = 1796.1955 1-4 EEL = 23323.4113 RESTRAINT = 0.0000 ESURF = 183.9281 minimization completed, ENE= -.10795936E+05 RMS= 0.172011E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0652E+04 1.7383E+01 1.2996E+02 C 6482 BOND = 1442.9468 ANGLE = 3679.9558 DIHED = 5429.0934 VDWAALS = -3878.0386 EEL = -34758.1370 EGB = -7937.0559 1-4 VDW = 1841.3694 1-4 EEL = 23343.8131 RESTRAINT = 0.0000 ESURF = 184.2668 minimization completed, ENE= -.10651786E+05 RMS= 0.173826E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0673E+04 1.7431E+01 1.0667E+02 N 3372 BOND = 1427.6427 ANGLE = 3782.6382 DIHED = 5371.3812 VDWAALS = -3902.3820 EEL = -34595.4046 EGB = -8006.9849 1-4 VDW = 1804.3921 1-4 EEL = 23259.5511 RESTRAINT = 0.0000 ESURF = 185.8189 minimization completed, ENE= -.10673347E+05 RMS= 0.174315E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0770E+04 1.7356E+01 1.1824E+02 N 1174 BOND = 1438.7238 ANGLE = 3662.4740 DIHED = 5385.0595 VDWAALS = -3890.3084 EEL = -34853.8911 EGB = -7898.2236 1-4 VDW = 1845.4321 1-4 EEL = 23354.7673 RESTRAINT = 0.0000 ESURF = 185.7631 minimization completed, ENE= -.10770203E+05 RMS= 0.173557E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0735E+04 1.7227E+01 1.0264E+02 N 4842 BOND = 1366.2885 ANGLE = 3738.8099 DIHED = 5417.9404 VDWAALS = -3878.1153 EEL = -34744.2564 EGB = -7884.5358 1-4 VDW = 1796.6839 1-4 EEL = 23268.2572 RESTRAINT = 0.0000 ESURF = 183.8242 minimization completed, ENE= -.10735104E+05 RMS= 0.172269E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0755E+04 1.7212E+01 1.1432E+02 C 5208 BOND = 1393.2653 ANGLE = 3742.9394 DIHED = 5401.9024 VDWAALS = -3902.0915 EEL = -34833.0930 EGB = -7916.0258 1-4 VDW = 1797.5090 1-4 EEL = 23376.8347 RESTRAINT = 0.0000 ESURF = 183.6127 minimization completed, ENE= -.10755147E+05 RMS= 0.172116E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0730E+04 1.7487E+01 1.3527E+02 C 2233 BOND = 1422.2309 ANGLE = 3695.6215 DIHED = 5430.2654 VDWAALS = -3879.4218 EEL = -34847.4829 EGB = -7871.3267 1-4 VDW = 1828.7451 1-4 EEL = 23308.0274 RESTRAINT = 0.0000 ESURF = 183.3685 minimization completed, ENE= -.10729973E+05 RMS= 0.174870E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0775E+04 1.7287E+01 1.1684E+02 C 1878 BOND = 1419.5242 ANGLE = 3755.2021 DIHED = 5398.9743 VDWAALS = -3960.5672 EEL = -34791.7368 EGB = -7830.7049 1-4 VDW = 1815.3547 1-4 EEL = 23235.2774 RESTRAINT = 0.0000 ESURF = 183.2185 minimization completed, ENE= -.10775458E+05 RMS= 0.172866E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0834E+04 1.7251E+01 1.0528E+02 C 589 BOND = 1399.2877 ANGLE = 3695.6935 DIHED = 5386.5304 VDWAALS = -3907.2366 EEL = -34614.8324 EGB = -8081.8986 1-4 VDW = 1785.1489 1-4 EEL = 23319.4291 RESTRAINT = 0.0000 ESURF = 183.9474 minimization completed, ENE= -.10833931E+05 RMS= 0.172510E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0709E+04 1.7401E+01 1.3885E+02 C 7264 BOND = 1406.7360 ANGLE = 3733.8328 DIHED = 5426.8038 VDWAALS = -3917.2204 EEL = -34856.1782 EGB = -7907.9108 1-4 VDW = 1786.2927 1-4 EEL = 23435.1827 RESTRAINT = 0.0000 ESURF = 183.2007 minimization completed, ENE= -.10709261E+05 RMS= 0.174013E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0716E+04 1.7219E+01 1.0928E+02 N 2643 BOND = 1405.5510 ANGLE = 3680.5475 DIHED = 5437.6375 VDWAALS = -3895.7888 EEL = -34691.2353 EGB = -8006.4107 1-4 VDW = 1796.5203 1-4 EEL = 23372.8449 RESTRAINT = 0.0000 ESURF = 184.7124 minimization completed, ENE= -.10715621E+05 RMS= 0.172188E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0796E+04 1.7388E+01 1.0693E+02 CG 598 BOND = 1422.3496 ANGLE = 3730.0547 DIHED = 5382.6358 VDWAALS = -3927.2389 EEL = -34636.3344 EGB = -8108.7131 1-4 VDW = 1795.2034 1-4 EEL = 23361.9872 RESTRAINT = 0.0000 ESURF = 184.1427 minimization completed, ENE= -.10795913E+05 RMS= 0.173876E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0794E+04 1.7314E+01 1.2664E+02 C 3097 BOND = 1369.7016 ANGLE = 3768.9208 DIHED = 5388.2205 VDWAALS = -3887.2539 EEL = -34715.9161 EGB = -7994.5157 1-4 VDW = 1809.0346 1-4 EEL = 23282.3632 RESTRAINT = 0.0000 ESURF = 185.1410 minimization completed, ENE= -.10794304E+05 RMS= 0.173144E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0699E+04 1.7406E+01 1.2561E+02 C 2064 BOND = 1425.4097 ANGLE = 3778.2338 DIHED = 5406.8563 VDWAALS = -3873.6612 EEL = -34863.3607 EGB = -7892.4104 1-4 VDW = 1796.8131 1-4 EEL = 23338.2353 RESTRAINT = 0.0000 ESURF = 184.7502 minimization completed, ENE= -.10699134E+05 RMS= 0.174058E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0825E+04 1.7205E+01 1.1758E+02 C 5622 BOND = 1402.4205 ANGLE = 3646.4038 DIHED = 5385.4553 VDWAALS = -3931.5660 EEL = -34697.6778 EGB = -8008.0240 1-4 VDW = 1808.5893 1-4 EEL = 23384.4417 RESTRAINT = 0.0000 ESURF = 184.7101 minimization completed, ENE= -.10825247E+05 RMS= 0.172051E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0808E+04 1.7360E+01 1.0185E+02 CA 2424 BOND = 1443.9880 ANGLE = 3679.7270 DIHED = 5373.0706 VDWAALS = -3907.4884 EEL = -34819.1361 EGB = -7888.5928 1-4 VDW = 1809.4693 1-4 EEL = 23315.9310 RESTRAINT = 0.0000 ESURF = 185.4769 minimization completed, ENE= -.10807555E+05 RMS= 0.173598E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0738E+04 1.7218E+01 1.1572E+02 CD 6140 BOND = 1430.4217 ANGLE = 3767.9343 DIHED = 5392.2475 VDWAALS = -3935.0624 EEL = -34704.6912 EGB = -7982.4812 1-4 VDW = 1800.1394 1-4 EEL = 23309.3192 RESTRAINT = 0.0000 ESURF = 184.0133 minimization completed, ENE= -.10738159E+05 RMS= 0.172183E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0660E+04 1.7414E+01 1.1261E+02 C 2886 BOND = 1408.3749 ANGLE = 3806.8426 DIHED = 5432.7177 VDWAALS = -3862.2984 EEL = -34915.4846 EGB = -7869.3366 1-4 VDW = 1778.5847 1-4 EEL = 23374.8733 RESTRAINT = 0.0000 ESURF = 185.4301 minimization completed, ENE= -.10660296E+05 RMS= 0.174145E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0727E+04 1.7311E+01 1.0913E+02 C 3157 BOND = 1348.8559 ANGLE = 3808.5718 DIHED = 5428.7512 VDWAALS = -3915.0540 EEL = -34833.0264 EGB = -7887.4343 1-4 VDW = 1823.4887 1-4 EEL = 23313.9303 RESTRAINT = 0.0000 ESURF = 185.4079 minimization completed, ENE= -.10726509E+05 RMS= 0.173110E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0708E+04 1.7390E+01 1.1259E+02 N 4699 BOND = 1384.4138 ANGLE = 3898.1920 DIHED = 5389.4102 VDWAALS = -3903.9244 EEL = -34950.4501 EGB = -7814.1543 1-4 VDW = 1799.5258 1-4 EEL = 23303.3945 RESTRAINT = 0.0000 ESURF = 185.4550 minimization completed, ENE= -.10708137E+05 RMS= 0.173905E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0663E+04 1.7281E+01 1.0338E+02 CA 6154 BOND = 1399.4369 ANGLE = 3733.0473 DIHED = 5432.7191 VDWAALS = -3853.5176 EEL = -34762.9730 EGB = -7975.1948 1-4 VDW = 1813.6603 1-4 EEL = 23362.1404 RESTRAINT = 0.0000 ESURF = 187.7709 minimization completed, ENE= -.10662910E+05 RMS= 0.172810E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0710E+04 1.7175E+01 1.1108E+02 N 3756 BOND = 1420.2621 ANGLE = 3762.7051 DIHED = 5448.1969 VDWAALS = -3931.1265 EEL = -34861.6903 EGB = -7830.3504 1-4 VDW = 1781.8116 1-4 EEL = 23315.3788 RESTRAINT = 0.0000 ESURF = 185.0393 minimization completed, ENE= -.10709773E+05 RMS= 0.171747E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0604E+04 1.7568E+01 1.1835E+02 C 7668 BOND = 1466.7298 ANGLE = 3777.1504 DIHED = 5450.3015 VDWAALS = -3898.1173 EEL = -34784.2054 EGB = -7914.0044 1-4 VDW = 1786.0189 1-4 EEL = 23327.0391 RESTRAINT = 0.0000 ESURF = 185.5543 minimization completed, ENE= -.10603533E+05 RMS= 0.175678E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 706.03 ( 7.66% of Gen B) | Calc gb diag 5470.08 (59.35% of Gen B) | Calc gb off-diag 3039.87 (32.98% of Gen B) | Gen Born time 9215.99 (100.0% of Nonbo) | Nonbond force 9215.99 (100.0% of Force) | Bond/Angle/Dihedral 8.16 ( 0.09% of Force) | Force time 9224.16 (100.0% of Runmd) | Runmd Time 9224.16 (98.35% of Total) | Other 155.07 ( 1.65% of Total) | Total time 9379.25 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 19:12:36.556 on 10/19/2010 | Setup done at 19:12:38.446 on 10/19/2010 | Run done at 21:48:55.810 on 10/19/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/19/2010 at 19:12:36 [-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 -1.0710E+04 1.7557E+01 1.2513E+02 C 5664 BOND = 1451.5444 ANGLE = 3758.0657 DIHED = 5444.7928 VDWAALS = -3931.9274 EEL = -34720.7027 EGB = -7960.0129 1-4 VDW = 1795.7429 1-4 EEL = 23269.2271 RESTRAINT = 0.0000 ESURF = 183.6186 minimization completed, ENE= -.10709652E+05 RMS= 0.175570E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0762E+04 1.7084E+01 1.0896E+02 C 2907 BOND = 1381.0752 ANGLE = 3762.6504 DIHED = 5433.3361 VDWAALS = -3968.0566 EEL = -34619.6699 EGB = -7993.6803 1-4 VDW = 1771.0915 1-4 EEL = 23287.6039 RESTRAINT = 0.0000 ESURF = 184.1422 minimization completed, ENE= -.10761508E+05 RMS= 0.170839E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0697E+04 1.7418E+01 1.0491E+02 C 6301 BOND = 1430.2324 ANGLE = 3739.7906 DIHED = 5455.8169 VDWAALS = -3964.8970 EEL = -34533.1250 EGB = -8043.5608 1-4 VDW = 1786.7453 1-4 EEL = 23248.4167 RESTRAINT = 0.0000 ESURF = 184.0426 minimization completed, ENE= -.10696538E+05 RMS= 0.174179E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0716E+04 1.7456E+01 1.1455E+02 C 6996 BOND = 1435.1097 ANGLE = 3770.6158 DIHED = 5443.0254 VDWAALS = -3932.7134 EEL = -34632.5336 EGB = -8073.7755 1-4 VDW = 1792.2139 1-4 EEL = 23296.2940 RESTRAINT = 0.0000 ESURF = 186.0859 minimization completed, ENE= -.10715678E+05 RMS= 0.174563E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0717E+04 1.7398E+01 1.1363E+02 C 5006 BOND = 1365.7421 ANGLE = 3737.4810 DIHED = 5455.7934 VDWAALS = -3984.4439 EEL = -34677.0038 EGB = -7957.4578 1-4 VDW = 1808.9187 1-4 EEL = 23350.5827 RESTRAINT = 0.0000 ESURF = 183.3723 minimization completed, ENE= -.10717015E+05 RMS= 0.173980E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0676E+04 1.7528E+01 1.0719E+02 N 3013 BOND = 1408.2631 ANGLE = 3803.0858 DIHED = 5425.5443 VDWAALS = -3955.9344 EEL = -34619.6852 EGB = -8001.8631 1-4 VDW = 1781.5146 1-4 EEL = 23300.1738 RESTRAINT = 0.0000 ESURF = 183.3648 minimization completed, ENE= -.10675536E+05 RMS= 0.175283E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0653E+04 1.7384E+01 1.1302E+02 C 3427 BOND = 1433.4636 ANGLE = 3784.4425 DIHED = 5430.3898 VDWAALS = -3947.7322 EEL = -34789.9176 EGB = -7905.3661 1-4 VDW = 1795.3598 1-4 EEL = 23361.9867 RESTRAINT = 0.0000 ESURF = 184.1971 minimization completed, ENE= -.10653176E+05 RMS= 0.173835E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0812E+04 1.7280E+01 1.0801E+02 CD 2779 BOND = 1414.8802 ANGLE = 3725.1073 DIHED = 5381.3928 VDWAALS = -3949.1256 EEL = -34765.4846 EGB = -7897.6683 1-4 VDW = 1783.7643 1-4 EEL = 23311.7279 RESTRAINT = 0.0000 ESURF = 183.4107 minimization completed, ENE= -.10811995E+05 RMS= 0.172798E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0827E+04 1.7405E+01 1.0900E+02 C 3907 BOND = 1432.9300 ANGLE = 3725.6218 DIHED = 5393.8334 VDWAALS = -3870.0110 EEL = -34845.0476 EGB = -7883.3361 1-4 VDW = 1782.6710 1-4 EEL = 23252.4175 RESTRAINT = 0.0000 ESURF = 183.6528 minimization completed, ENE= -.10827268E+05 RMS= 0.174047E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0777E+04 1.7221E+01 1.0484E+02 C 6077 BOND = 1376.0763 ANGLE = 3735.7368 DIHED = 5416.6149 VDWAALS = -3972.6924 EEL = -34793.8624 EGB = -7853.5012 1-4 VDW = 1817.4917 1-4 EEL = 23315.0268 RESTRAINT = 0.0000 ESURF = 182.3143 minimization completed, ENE= -.10776795E+05 RMS= 0.172205E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0722E+04 1.7431E+01 1.0508E+02 C 3274 BOND = 1458.6258 ANGLE = 3698.7637 DIHED = 5398.9771 VDWAALS = -3887.9006 EEL = -34801.4581 EGB = -7882.1309 1-4 VDW = 1803.9820 1-4 EEL = 23306.4431 RESTRAINT = 0.0000 ESURF = 182.6567 minimization completed, ENE= -.10722041E+05 RMS= 0.174306E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0741E+04 1.7368E+01 1.0106E+02 C 3739 BOND = 1416.3594 ANGLE = 3706.6899 DIHED = 5419.6860 VDWAALS = -3939.7030 EEL = -34819.3195 EGB = -7848.2270 1-4 VDW = 1810.3620 1-4 EEL = 23329.7187 RESTRAINT = 0.0000 ESURF = 183.7222 minimization completed, ENE= -.10740711E+05 RMS= 0.173684E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0841E+04 1.7108E+01 1.1737E+02 N 1351 BOND = 1388.2274 ANGLE = 3713.3015 DIHED = 5385.9637 VDWAALS = -3901.2827 EEL = -34927.4836 EGB = -7760.6191 1-4 VDW = 1806.1319 1-4 EEL = 23271.3527 RESTRAINT = 0.0000 ESURF = 183.6049 minimization completed, ENE= -.10840803E+05 RMS= 0.171078E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0733E+04 1.7423E+01 1.1744E+02 CZ 4241 BOND = 1444.3138 ANGLE = 3778.7240 DIHED = 5411.4967 VDWAALS = -3976.2735 EEL = -34785.3877 EGB = -7839.7597 1-4 VDW = 1789.6670 1-4 EEL = 23261.3977 RESTRAINT = 0.0000 ESURF = 183.2205 minimization completed, ENE= -.10732601E+05 RMS= 0.174227E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0794E+04 1.7177E+01 1.3347E+02 C 6327 BOND = 1406.9902 ANGLE = 3712.2015 DIHED = 5431.4797 VDWAALS = -3895.2886 EEL = -34878.4199 EGB = -7854.1982 1-4 VDW = 1806.7809 1-4 EEL = 23291.7506 RESTRAINT = 0.0000 ESURF = 184.2468 minimization completed, ENE= -.10794457E+05 RMS= 0.171774E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0674E+04 1.7360E+01 1.1584E+02 C 4840 BOND = 1414.8479 ANGLE = 3772.7217 DIHED = 5382.9331 VDWAALS = -3933.2690 EEL = -34825.7754 EGB = -7855.2649 1-4 VDW = 1811.4401 1-4 EEL = 23373.3730 RESTRAINT = 0.0000 ESURF = 184.8371 minimization completed, ENE= -.10674156E+05 RMS= 0.173602E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0600E+04 1.7453E+01 1.0792E+02 CA 2930 BOND = 1475.5308 ANGLE = 3735.0133 DIHED = 5431.4185 VDWAALS = -3875.8079 EEL = -34815.7542 EGB = -7915.1495 1-4 VDW = 1828.7762 1-4 EEL = 23349.2232 RESTRAINT = 0.0000 ESURF = 186.3878 minimization completed, ENE= -.10600362E+05 RMS= 0.174533E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0744E+04 1.7120E+01 1.0607E+02 CD 7727 BOND = 1364.0082 ANGLE = 3748.8620 DIHED = 5425.0251 VDWAALS = -3886.7225 EEL = -34805.9628 EGB = -7891.6896 1-4 VDW = 1822.4226 1-4 EEL = 23293.4336 RESTRAINT = 0.0000 ESURF = 186.5713 minimization completed, ENE= -.10744052E+05 RMS= 0.171202E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0727E+04 1.7357E+01 1.1022E+02 C 450 BOND = 1463.3796 ANGLE = 3764.0092 DIHED = 5362.9221 VDWAALS = -3875.9764 EEL = -34782.4289 EGB = -7887.9659 1-4 VDW = 1785.6959 1-4 EEL = 23255.6534 RESTRAINT = 0.0000 ESURF = 187.5987 minimization completed, ENE= -.10727112E+05 RMS= 0.173574E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0613E+04 1.7442E+01 1.1314E+02 C 6360 BOND = 1390.2410 ANGLE = 3906.8219 DIHED = 5407.3164 VDWAALS = -3877.6481 EEL = -34905.8502 EGB = -7864.9836 1-4 VDW = 1802.7341 1-4 EEL = 23342.7268 RESTRAINT = 0.0000 ESURF = 186.0103 minimization completed, ENE= -.10612631E+05 RMS= 0.174421E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0762E+04 1.7212E+01 1.1515E+02 C 2019 BOND = 1425.7830 ANGLE = 3683.8866 DIHED = 5415.8297 VDWAALS = -3882.0517 EEL = -34923.9806 EGB = -7849.6431 1-4 VDW = 1819.5494 1-4 EEL = 23362.0134 RESTRAINT = 0.0000 ESURF = 186.5110 minimization completed, ENE= -.10762102E+05 RMS= 0.172119E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0851E+04 1.7257E+01 1.3634E+02 CD 7219 BOND = 1354.8146 ANGLE = 3644.1202 DIHED = 5400.9680 VDWAALS = -3888.0262 EEL = -34783.2116 EGB = -7847.1777 1-4 VDW = 1829.9870 1-4 EEL = 23252.1986 RESTRAINT = 0.0000 ESURF = 185.1398 minimization completed, ENE= -.10851187E+05 RMS= 0.172565E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0795E+04 1.7327E+01 1.2803E+02 C 6317 BOND = 1449.5790 ANGLE = 3703.8693 DIHED = 5373.5930 VDWAALS = -3885.7089 EEL = -34907.7809 EGB = -7746.3159 1-4 VDW = 1779.3488 1-4 EEL = 23253.3974 RESTRAINT = 0.0000 ESURF = 184.5950 minimization completed, ENE= -.10795423E+05 RMS= 0.173272E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0775E+04 1.7400E+01 1.1592E+02 C 1718 BOND = 1459.0627 ANGLE = 3683.4132 DIHED = 5442.1505 VDWAALS = -3910.5953 EEL = -34953.9285 EGB = -7689.9573 1-4 VDW = 1782.0847 1-4 EEL = 23228.9981 RESTRAINT = 0.0000 ESURF = 184.0235 minimization completed, ENE= -.10774749E+05 RMS= 0.173997E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0714E+04 1.7526E+01 1.1730E+02 CD 7204 BOND = 1463.3000 ANGLE = 3761.6211 DIHED = 5364.3597 VDWAALS = -3878.2693 EEL = -34923.1880 EGB = -7747.0836 1-4 VDW = 1796.4362 1-4 EEL = 23266.0514 RESTRAINT = 0.0000 ESURF = 182.6826 minimization completed, ENE= -.10714090E+05 RMS= 0.175256E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0721E+04 1.7157E+01 1.1750E+02 CD 3135 BOND = 1412.6437 ANGLE = 3716.5491 DIHED = 5427.9105 VDWAALS = -3912.2266 EEL = -34855.5380 EGB = -7798.2158 1-4 VDW = 1793.2848 1-4 EEL = 23309.1850 RESTRAINT = 0.0000 ESURF = 185.0150 minimization completed, ENE= -.10721392E+05 RMS= 0.171573E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0672E+04 1.7367E+01 1.0806E+02 C 5285 BOND = 1467.2881 ANGLE = 3750.5397 DIHED = 5416.0111 VDWAALS = -3953.8772 EEL = -34835.6269 EGB = -7744.7763 1-4 VDW = 1777.0946 1-4 EEL = 23268.0797 RESTRAINT = 0.0000 ESURF = 182.7676 minimization completed, ENE= -.10672500E+05 RMS= 0.173673E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0710E+04 1.7357E+01 1.1184E+02 PG 7838 BOND = 1439.4394 ANGLE = 3777.2061 DIHED = 5419.4000 VDWAALS = -3958.0262 EEL = -34804.7362 EGB = -7840.1567 1-4 VDW = 1790.2562 1-4 EEL = 23283.0913 RESTRAINT = 0.0000 ESURF = 183.5391 minimization completed, ENE= -.10709987E+05 RMS= 0.173568E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0806E+04 1.7343E+01 1.0112E+02 CA 708 BOND = 1470.0635 ANGLE = 3649.3580 DIHED = 5382.8113 VDWAALS = -3957.8962 EEL = -34914.1594 EGB = -7765.4721 1-4 VDW = 1819.5555 1-4 EEL = 23327.0911 RESTRAINT = 0.0000 ESURF = 182.5749 minimization completed, ENE= -.10806074E+05 RMS= 0.173427E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0724E+04 1.7276E+01 1.0482E+02 CD 5261 BOND = 1391.6975 ANGLE = 3722.9730 DIHED = 5472.5830 VDWAALS = -3930.1342 EEL = -35039.0296 EGB = -7622.1716 1-4 VDW = 1796.9526 1-4 EEL = 23302.2973 RESTRAINT = 0.0000 ESURF = 180.8710 minimization completed, ENE= -.10723961E+05 RMS= 0.172763E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0635E+04 1.7380E+01 1.1470E+02 CA 3695 BOND = 1459.9568 ANGLE = 3810.7126 DIHED = 5433.1500 VDWAALS = -3952.8441 EEL = -34952.0399 EGB = -7664.2755 1-4 VDW = 1794.0446 1-4 EEL = 23254.1559 RESTRAINT = 0.0000 ESURF = 182.6144 minimization completed, ENE= -.10634525E+05 RMS= 0.173800E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0727E+04 1.7447E+01 1.0284E+02 CZ 6666 BOND = 1408.5374 ANGLE = 3802.6070 DIHED = 5419.3747 VDWAALS = -3976.7340 EEL = -35125.2412 EGB = -7562.8927 1-4 VDW = 1814.9041 1-4 EEL = 23309.8807 RESTRAINT = 0.0000 ESURF = 182.0644 minimization completed, ENE= -.10727500E+05 RMS= 0.174473E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0803E+04 1.7295E+01 1.1729E+02 CD 4614 BOND = 1414.6533 ANGLE = 3712.2362 DIHED = 5398.4015 VDWAALS = -3907.8858 EEL = -34990.0921 EGB = -7719.4078 1-4 VDW = 1799.2047 1-4 EEL = 23307.1855 RESTRAINT = 0.0000 ESURF = 182.6652 minimization completed, ENE= -.10803039E+05 RMS= 0.172945E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0768E+04 1.7401E+01 1.2483E+02 C 4784 BOND = 1438.1104 ANGLE = 3776.7428 DIHED = 5399.3331 VDWAALS = -3912.5008 EEL = -34687.2062 EGB = -7951.0140 1-4 VDW = 1806.5903 1-4 EEL = 23178.6888 RESTRAINT = 0.0000 ESURF = 182.9908 minimization completed, ENE= -.10768265E+05 RMS= 0.174008E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0694E+04 1.7360E+01 1.4182E+02 C 6700 BOND = 1390.2163 ANGLE = 3763.0625 DIHED = 5398.7337 VDWAALS = -3906.8467 EEL = -34878.2033 EGB = -7779.0898 1-4 VDW = 1806.5026 1-4 EEL = 23326.8604 RESTRAINT = 0.0000 ESURF = 185.1325 minimization completed, ENE= -.10693632E+05 RMS= 0.173595E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0662E+04 1.7264E+01 1.0195E+02 CD 3751 BOND = 1368.4201 ANGLE = 3815.5137 DIHED = 5431.4845 VDWAALS = -3904.9687 EEL = -34959.2726 EGB = -7706.4048 1-4 VDW = 1797.2236 1-4 EEL = 23312.0735 RESTRAINT = 0.0000 ESURF = 183.4779 minimization completed, ENE= -.10662453E+05 RMS= 0.172635E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0719E+04 1.7357E+01 1.0626E+02 CD 3186 BOND = 1436.8304 ANGLE = 3745.4805 DIHED = 5461.5790 VDWAALS = -3939.3717 EEL = -34985.4952 EGB = -7720.8815 1-4 VDW = 1786.6406 1-4 EEL = 23313.1090 RESTRAINT = 0.0000 ESURF = 183.5163 minimization completed, ENE= -.10718592E+05 RMS= 0.173573E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0756E+04 1.7324E+01 1.1033E+02 CG 6398 BOND = 1406.6699 ANGLE = 3722.6675 DIHED = 5402.2035 VDWAALS = -3911.3181 EEL = -34980.5376 EGB = -7717.3664 1-4 VDW = 1804.5151 1-4 EEL = 23333.2973 RESTRAINT = 0.0000 ESURF = 184.3460 minimization completed, ENE= -.10755523E+05 RMS= 0.173242E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0701E+04 1.7215E+01 1.1707E+02 C 4224 BOND = 1343.8985 ANGLE = 3823.8702 DIHED = 5430.8495 VDWAALS = -3939.5737 EEL = -35039.8278 EGB = -7689.9200 1-4 VDW = 1811.7819 1-4 EEL = 23372.8511 RESTRAINT = 0.0000 ESURF = 185.3354 minimization completed, ENE= -.10700735E+05 RMS= 0.172151E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0778E+04 1.7185E+01 1.0956E+02 CG 369 BOND = 1410.1531 ANGLE = 3706.2213 DIHED = 5418.1910 VDWAALS = -3924.3007 EEL = -34904.8185 EGB = -7783.7299 1-4 VDW = 1811.5668 1-4 EEL = 23305.5473 RESTRAINT = 0.0000 ESURF = 183.6396 minimization completed, ENE= -.10777530E+05 RMS= 0.171855E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0759E+04 1.7460E+01 1.1379E+02 C 2806 BOND = 1400.7851 ANGLE = 3793.6211 DIHED = 5367.9590 VDWAALS = -3948.9289 EEL = -34837.3228 EGB = -7872.4024 1-4 VDW = 1784.4655 1-4 EEL = 23368.9552 RESTRAINT = 0.0000 ESURF = 184.2345 minimization completed, ENE= -.10758634E+05 RMS= 0.174596E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0800E+04 1.7226E+01 1.1812E+02 CA 1160 BOND = 1373.2850 ANGLE = 3700.1788 DIHED = 5432.4486 VDWAALS = -3927.1396 EEL = -34904.1049 EGB = -7740.1447 1-4 VDW = 1801.0404 1-4 EEL = 23280.4927 RESTRAINT = 0.0000 ESURF = 183.5875 minimization completed, ENE= -.10800356E+05 RMS= 0.172264E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0683E+04 1.7496E+01 1.1055E+02 C 6327 BOND = 1419.6242 ANGLE = 3745.1904 DIHED = 5428.9976 VDWAALS = -3900.9742 EEL = -34766.6553 EGB = -7939.2711 1-4 VDW = 1818.2415 1-4 EEL = 23325.9027 RESTRAINT = 0.0000 ESURF = 185.5392 minimization completed, ENE= -.10683405E+05 RMS= 0.174958E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0741E+04 1.7463E+01 1.0975E+02 CD 3169 BOND = 1438.0558 ANGLE = 3750.0197 DIHED = 5390.6254 VDWAALS = -3934.4334 EEL = -34889.5800 EGB = -7723.7856 1-4 VDW = 1804.6868 1-4 EEL = 23238.7802 RESTRAINT = 0.0000 ESURF = 184.3420 minimization completed, ENE= -.10741289E+05 RMS= 0.174628E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0740E+04 1.7451E+01 1.2130E+02 C 6782 BOND = 1425.4573 ANGLE = 3684.5516 DIHED = 5412.6944 VDWAALS = -3920.8736 EEL = -34992.5247 EGB = -7717.9743 1-4 VDW = 1797.8818 1-4 EEL = 23386.4396 RESTRAINT = 0.0000 ESURF = 183.9897 minimization completed, ENE= -.10740358E+05 RMS= 0.174507E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0658E+04 1.7422E+01 1.0833E+02 C 5069 BOND = 1398.9853 ANGLE = 3867.5683 DIHED = 5417.9476 VDWAALS = -3926.9834 EEL = -34890.0586 EGB = -7807.4446 1-4 VDW = 1793.1460 1-4 EEL = 23305.9361 RESTRAINT = 0.0000 ESURF = 182.8502 minimization completed, ENE= -.10658053E+05 RMS= 0.174220E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0742E+04 1.7332E+01 1.3336E+02 C 3819 BOND = 1396.1738 ANGLE = 3713.4209 DIHED = 5428.2030 VDWAALS = -3931.2191 EEL = -34894.7677 EGB = -7802.7348 1-4 VDW = 1817.3674 1-4 EEL = 23350.4197 RESTRAINT = 0.0000 ESURF = 181.4652 minimization completed, ENE= -.10741671E+05 RMS= 0.173319E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0745E+04 1.7310E+01 1.1920E+02 C 7578 BOND = 1421.0426 ANGLE = 3684.5722 DIHED = 5430.4754 VDWAALS = -3882.1309 EEL = -35099.1289 EGB = -7682.5556 1-4 VDW = 1803.2629 1-4 EEL = 23395.9141 RESTRAINT = 0.0000 ESURF = 183.8045 minimization completed, ENE= -.10744744E+05 RMS= 0.173096E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0747E+04 1.7311E+01 1.0803E+02 N 7083 BOND = 1396.0612 ANGLE = 3726.0805 DIHED = 5401.3535 VDWAALS = -3868.9976 EEL = -34961.3346 EGB = -7761.2669 1-4 VDW = 1817.9970 1-4 EEL = 23318.7785 RESTRAINT = 0.0000 ESURF = 184.4372 minimization completed, ENE= -.10746891E+05 RMS= 0.173106E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0751E+04 1.7387E+01 1.0534E+02 C 2256 BOND = 1422.8605 ANGLE = 3751.1402 DIHED = 5430.0944 VDWAALS = -3932.6805 EEL = -34809.4499 EGB = -7881.4735 1-4 VDW = 1814.2480 1-4 EEL = 23268.6550 RESTRAINT = 0.0000 ESURF = 185.1942 minimization completed, ENE= -.10751412E+05 RMS= 0.173873E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 709.08 ( 7.69% of Gen B) | Calc gb diag 5486.90 (59.54% of Gen B) | Calc gb off-diag 3019.87 (32.77% of Gen B) | Gen Born time 9215.84 (100.0% of Nonbo) | Nonbond force 9215.84 (100.0% of Force) | Bond/Angle/Dihedral 6.76 ( 0.07% of Force) | Force time 9222.61 (100.0% of Runmd) | Runmd Time 9222.61 (98.98% of Total) | Other 94.69 ( 1.02% of Total) | Total time 9317.33 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 19:12:36.561 on 10/19/2010 | Setup done at 19:12:37.273 on 10/19/2010 | Run done at 21:47:53.888 on 10/19/2010 | wallclock() was called 1809 times ------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 10/19/2010 at 19:12:36 [-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 -1.0744E+04 1.7269E+01 1.2080E+02 C 7452 BOND = 1407.2780 ANGLE = 3773.0304 DIHED = 5408.2717 VDWAALS = -3863.1845 EEL = -35012.5234 EGB = -7713.5777 1-4 VDW = 1792.6084 1-4 EEL = 23278.9175 RESTRAINT = 0.0000 ESURF = 185.0297 minimization completed, ENE= -.10744150E+05 RMS= 0.172688E+02 minimizing coord set # 2 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0802E+04 1.7327E+01 1.0102E+02 C 2514 BOND = 1447.7923 ANGLE = 3757.0836 DIHED = 5401.2193 VDWAALS = -3893.6435 EEL = -35063.8628 EGB = -7704.1608 1-4 VDW = 1767.3297 1-4 EEL = 23301.8036 RESTRAINT = 0.0000 ESURF = 184.2470 minimization completed, ENE= -.10802192E+05 RMS= 0.173265E+02 minimizing coord set # 3 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0623E+04 1.7370E+01 1.0655E+02 CG 4706 BOND = 1423.3378 ANGLE = 3856.4572 DIHED = 5458.5816 VDWAALS = -3870.3024 EEL = -34990.8777 EGB = -7746.1352 1-4 VDW = 1793.6500 1-4 EEL = 23268.8359 RESTRAINT = 0.0000 ESURF = 183.5905 minimization completed, ENE= -.10622862E+05 RMS= 0.173702E+02 minimizing coord set # 4 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0729E+04 1.7314E+01 1.0742E+02 C 4544 BOND = 1423.4636 ANGLE = 3718.5489 DIHED = 5427.0961 VDWAALS = -3907.6013 EEL = -34994.3886 EGB = -7703.8348 1-4 VDW = 1802.6799 1-4 EEL = 23321.8369 RESTRAINT = 0.0000 ESURF = 183.4407 minimization completed, ENE= -.10728759E+05 RMS= 0.173135E+02 minimizing coord set # 5 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0883E+04 1.6988E+01 1.1271E+02 CZ 2872 BOND = 1384.1830 ANGLE = 3664.3663 DIHED = 5410.9714 VDWAALS = -3965.4144 EEL = -34858.9787 EGB = -7814.9539 1-4 VDW = 1809.8723 1-4 EEL = 23301.7251 RESTRAINT = 0.0000 ESURF = 185.4377 minimization completed, ENE= -.10882791E+05 RMS= 0.169879E+02 minimizing coord set # 6 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0671E+04 1.7165E+01 1.1045E+02 C 4808 BOND = 1363.3785 ANGLE = 3789.6884 DIHED = 5411.0241 VDWAALS = -3919.4316 EEL = -34920.1687 EGB = -7772.0508 1-4 VDW = 1826.5572 1-4 EEL = 23365.1462 RESTRAINT = 0.0000 ESURF = 184.7189 minimization completed, ENE= -.10671138E+05 RMS= 0.171648E+02 minimizing coord set # 7 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0682E+04 1.7513E+01 1.3635E+02 CD 2511 BOND = 1468.2765 ANGLE = 3716.0132 DIHED = 5454.3331 VDWAALS = -3898.0850 EEL = -34913.7990 EGB = -7758.4814 1-4 VDW = 1788.6415 1-4 EEL = 23273.8321 RESTRAINT = 0.0000 ESURF = 186.8953 minimization completed, ENE= -.10682374E+05 RMS= 0.175134E+02 minimizing coord set # 8 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0631E+04 1.7483E+01 1.2041E+02 C 4859 BOND = 1418.6647 ANGLE = 3805.7303 DIHED = 5441.7283 VDWAALS = -3850.6561 EEL = -35153.2193 EGB = -7623.7260 1-4 VDW = 1807.8666 1-4 EEL = 23337.4665 RESTRAINT = 0.0000 ESURF = 185.1066 minimization completed, ENE= -.10631038E+05 RMS= 0.174832E+02 minimizing coord set # 9 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0695E+04 1.7365E+01 1.1705E+02 N 1327 BOND = 1422.0521 ANGLE = 3774.2484 DIHED = 5419.8016 VDWAALS = -3898.6054 EEL = -34875.8764 EGB = -7842.3108 1-4 VDW = 1813.0752 1-4 EEL = 23307.1250 RESTRAINT = 0.0000 ESURF = 185.0999 minimization completed, ENE= -.10695390E+05 RMS= 0.173646E+02 minimizing coord set # 10 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0714E+04 1.7379E+01 1.0632E+02 C 1059 BOND = 1411.9352 ANGLE = 3778.7771 DIHED = 5404.5141 VDWAALS = -3910.6123 EEL = -34770.6305 EGB = -7891.3324 1-4 VDW = 1807.8804 1-4 EEL = 23269.1798 RESTRAINT = 0.0000 ESURF = 186.1335 minimization completed, ENE= -.10714155E+05 RMS= 0.173794E+02 minimizing coord set # 11 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0597E+04 1.7466E+01 9.7463E+01 C 5608 BOND = 1445.9912 ANGLE = 3848.7907 DIHED = 5451.1604 VDWAALS = -3901.2538 EEL = -34800.2976 EGB = -7884.2426 1-4 VDW = 1789.5674 1-4 EEL = 23267.9343 RESTRAINT = 0.0000 ESURF = 185.1177 minimization completed, ENE= -.10597232E+05 RMS= 0.174658E+02 minimizing coord set # 12 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0669E+04 1.7417E+01 1.4089E+02 C 512 BOND = 1422.5014 ANGLE = 3797.6541 DIHED = 5411.5353 VDWAALS = -3873.6586 EEL = -34786.7076 EGB = -7957.5343 1-4 VDW = 1795.0335 1-4 EEL = 23335.4774 RESTRAINT = 0.0000 ESURF = 186.3890 minimization completed, ENE= -.10669310E+05 RMS= 0.174171E+02 minimizing coord set # 13 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0858E+04 1.7129E+01 1.0846E+02 C 2855 BOND = 1377.2212 ANGLE = 3672.1819 DIHED = 5400.1689 VDWAALS = -3894.0468 EEL = -34760.3128 EGB = -7947.0826 1-4 VDW = 1779.0434 1-4 EEL = 23330.1061 RESTRAINT = 0.0000 ESURF = 185.2179 minimization completed, ENE= -.10857503E+05 RMS= 0.171292E+02 minimizing coord set # 14 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0806E+04 1.7354E+01 1.1337E+02 C 6077 BOND = 1421.5318 ANGLE = 3724.3309 DIHED = 5389.9123 VDWAALS = -3920.3222 EEL = -34885.8314 EGB = -7841.3352 1-4 VDW = 1783.0087 1-4 EEL = 23338.9926 RESTRAINT = 0.0000 ESURF = 183.6005 minimization completed, ENE= -.10806112E+05 RMS= 0.173538E+02 minimizing coord set # 15 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0700E+04 1.7326E+01 1.3100E+02 C 7026 BOND = 1408.4958 ANGLE = 3789.3416 DIHED = 5415.7483 VDWAALS = -3920.8564 EEL = -34807.4462 EGB = -7862.3326 1-4 VDW = 1783.3650 1-4 EEL = 23308.7888 RESTRAINT = 0.0000 ESURF = 185.1089 minimization completed, ENE= -.10699787E+05 RMS= 0.173257E+02 minimizing coord set # 16 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0668E+04 1.7536E+01 1.1075E+02 C 6604 BOND = 1448.2380 ANGLE = 3768.1959 DIHED = 5384.1758 VDWAALS = -3871.8763 EEL = -34617.7267 EGB = -8009.3176 1-4 VDW = 1809.8547 1-4 EEL = 23234.5630 RESTRAINT = 0.0000 ESURF = 185.8753 minimization completed, ENE= -.10668018E+05 RMS= 0.175361E+02 minimizing coord set # 17 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0759E+04 1.7282E+01 1.1824E+02 CD 7727 BOND = 1425.6356 ANGLE = 3721.8527 DIHED = 5411.9750 VDWAALS = -3878.9194 EEL = -34809.9969 EGB = -7930.0919 1-4 VDW = 1793.3823 1-4 EEL = 23321.1619 RESTRAINT = 0.0000 ESURF = 186.4977 minimization completed, ENE= -.10758503E+05 RMS= 0.172817E+02 minimizing coord set # 18 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0741E+04 1.7477E+01 1.1806E+02 CA 2883 BOND = 1394.3868 ANGLE = 3731.6136 DIHED = 5373.3503 VDWAALS = -3886.9278 EEL = -34790.3727 EGB = -7858.5004 1-4 VDW = 1824.2634 1-4 EEL = 23287.3205 RESTRAINT = 0.0000 ESURF = 183.8719 minimization completed, ENE= -.10740994E+05 RMS= 0.174767E+02 minimizing coord set # 19 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0716E+04 1.7552E+01 1.1083E+02 C 278 BOND = 1460.9736 ANGLE = 3754.4090 DIHED = 5377.0913 VDWAALS = -3947.5980 EEL = -34696.2775 EGB = -7945.5447 1-4 VDW = 1792.5185 1-4 EEL = 23303.6259 RESTRAINT = 0.0000 ESURF = 184.3084 minimization completed, ENE= -.10716493E+05 RMS= 0.175516E+02 minimizing coord set # 20 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0714E+04 1.7259E+01 1.5210E+02 C 1978 BOND = 1405.6477 ANGLE = 3823.7661 DIHED = 5397.4446 VDWAALS = -3930.0331 EEL = -34814.0430 EGB = -7790.9742 1-4 VDW = 1796.9982 1-4 EEL = 23214.2458 RESTRAINT = 0.0000 ESURF = 183.1757 minimization completed, ENE= -.10713772E+05 RMS= 0.172589E+02 minimizing coord set # 21 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0714E+04 1.7401E+01 1.1557E+02 CG 961 BOND = 1416.3610 ANGLE = 3791.9567 DIHED = 5396.8268 VDWAALS = -3943.8396 EEL = -34743.8245 EGB = -7893.2054 1-4 VDW = 1801.9912 1-4 EEL = 23276.1987 RESTRAINT = 0.0000 ESURF = 183.3510 minimization completed, ENE= -.10714184E+05 RMS= 0.174008E+02 minimizing coord set # 22 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0719E+04 1.7203E+01 9.9248E+01 CZ 3985 BOND = 1400.5723 ANGLE = 3677.8026 DIHED = 5451.5324 VDWAALS = -3905.3528 EEL = -34645.5553 EGB = -8008.1199 1-4 VDW = 1817.0119 1-4 EEL = 23306.9919 RESTRAINT = 0.0000 ESURF = 186.3619 minimization completed, ENE= -.10718755E+05 RMS= 0.172031E+02 minimizing coord set # 23 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0653E+04 1.7584E+01 1.3123E+02 C 4649 BOND = 1458.8996 ANGLE = 3742.0255 DIHED = 5403.7249 VDWAALS = -3916.2938 EEL = -34636.4271 EGB = -8052.9697 1-4 VDW = 1816.7169 1-4 EEL = 23344.9842 RESTRAINT = 0.0000 ESURF = 186.5610 minimization completed, ENE= -.10652779E+05 RMS= 0.175844E+02 minimizing coord set # 24 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0728E+04 1.7205E+01 1.3094E+02 CG 1287 BOND = 1436.7243 ANGLE = 3745.6721 DIHED = 5433.9455 VDWAALS = -3918.0130 EEL = -34811.5983 EGB = -7894.4787 1-4 VDW = 1800.3101 1-4 EEL = 23293.8128 RESTRAINT = 0.0000 ESURF = 185.9446 minimization completed, ENE= -.10727681E+05 RMS= 0.172047E+02 minimizing coord set # 25 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0663E+04 1.7439E+01 1.1664E+02 C 1225 BOND = 1401.9562 ANGLE = 3843.9599 DIHED = 5446.0534 VDWAALS = -3930.1897 EEL = -34782.2998 EGB = -7863.4337 1-4 VDW = 1788.1115 1-4 EEL = 23249.9409 RESTRAINT = 0.0000 ESURF = 182.9763 minimization completed, ENE= -.10662925E+05 RMS= 0.174386E+02 minimizing coord set # 26 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0765E+04 1.7620E+01 1.0847E+02 CD 5859 BOND = 1426.5702 ANGLE = 3721.9923 DIHED = 5413.7325 VDWAALS = -3922.4581 EEL = -34971.4747 EGB = -7775.6023 1-4 VDW = 1815.1591 1-4 EEL = 23342.8070 RESTRAINT = 0.0000 ESURF = 184.4665 minimization completed, ENE= -.10764807E+05 RMS= 0.176203E+02 minimizing coord set # 27 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0671E+04 1.7670E+01 1.0472E+02 N 317 BOND = 1493.1791 ANGLE = 3716.9461 DIHED = 5402.4472 VDWAALS = -3918.0350 EEL = -34644.7616 EGB = -7936.2861 1-4 VDW = 1809.4776 1-4 EEL = 23220.9346 RESTRAINT = 0.0000 ESURF = 185.0102 minimization completed, ENE= -.10671088E+05 RMS= 0.176697E+02 minimizing coord set # 28 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0701E+04 1.7373E+01 1.2388E+02 CG 2253 BOND = 1421.3104 ANGLE = 3758.9237 DIHED = 5441.3913 VDWAALS = -3960.3534 EEL = -34668.6833 EGB = -7973.5439 1-4 VDW = 1795.4291 1-4 EEL = 23300.5332 RESTRAINT = 0.0000 ESURF = 183.9642 minimization completed, ENE= -.10701029E+05 RMS= 0.173732E+02 minimizing coord set # 29 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0608E+04 1.7220E+01 1.1631E+02 C5 7862 BOND = 1359.6718 ANGLE = 3847.5466 DIHED = 5452.3041 VDWAALS = -3923.2947 EEL = -34787.0348 EGB = -7850.5391 1-4 VDW = 1808.8562 1-4 EEL = 23301.0658 RESTRAINT = 0.0000 ESURF = 183.7392 minimization completed, ENE= -.10607685E+05 RMS= 0.172199E+02 minimizing coord set # 30 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0625E+04 1.7245E+01 1.1335E+02 CD 6712 BOND = 1410.0188 ANGLE = 3833.1166 DIHED = 5421.7705 VDWAALS = -3940.2811 EEL = -34760.9104 EGB = -7846.4917 1-4 VDW = 1806.6331 1-4 EEL = 23268.6599 RESTRAINT = 0.0000 ESURF = 182.4243 minimization completed, ENE= -.10625060E+05 RMS= 0.172452E+02 minimizing coord set # 31 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0806E+04 1.7225E+01 1.0005E+02 CG 5392 BOND = 1395.4221 ANGLE = 3684.2496 DIHED = 5374.9056 VDWAALS = -3944.4777 EEL = -34665.2109 EGB = -7879.9521 1-4 VDW = 1803.0438 1-4 EEL = 23242.5122 RESTRAINT = 0.0000 ESURF = 183.7028 minimization completed, ENE= -.10805805E+05 RMS= 0.172254E+02 minimizing coord set # 32 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0706E+04 1.7055E+01 1.1152E+02 C 2019 BOND = 1407.8248 ANGLE = 3751.0565 DIHED = 5413.0734 VDWAALS = -3982.3247 EEL = -34832.3562 EGB = -7714.1915 1-4 VDW = 1799.4837 1-4 EEL = 23269.6696 RESTRAINT = 0.0000 ESURF = 182.2593 minimization completed, ENE= -.10705505E+05 RMS= 0.170545E+02 minimizing coord set # 33 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0711E+04 1.7388E+01 1.2335E+02 C 5492 BOND = 1394.4077 ANGLE = 3715.1764 DIHED = 5404.5773 VDWAALS = -3998.4665 EEL = -34802.0507 EGB = -7826.2785 1-4 VDW = 1833.7749 1-4 EEL = 23385.2682 RESTRAINT = 0.0000 ESURF = 182.8350 minimization completed, ENE= -.10710756E+05 RMS= 0.173877E+02 minimizing coord set # 34 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0755E+04 1.7407E+01 1.0406E+02 N 692 BOND = 1389.1953 ANGLE = 3749.5246 DIHED = 5441.3020 VDWAALS = -3919.8586 EEL = -35062.0491 EGB = -7649.7980 1-4 VDW = 1802.8378 1-4 EEL = 23309.7608 RESTRAINT = 0.0000 ESURF = 183.6739 minimization completed, ENE= -.10755411E+05 RMS= 0.174072E+02 minimizing coord set # 35 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0751E+04 1.7276E+01 1.1107E+02 C 4018 BOND = 1383.5954 ANGLE = 3719.2077 DIHED = 5441.3644 VDWAALS = -3949.8524 EEL = -34686.4792 EGB = -7895.9554 1-4 VDW = 1802.6811 1-4 EEL = 23249.1428 RESTRAINT = 0.0000 ESURF = 184.8429 minimization completed, ENE= -.10751453E+05 RMS= 0.172756E+02 minimizing coord set # 36 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0706E+04 1.7392E+01 1.1267E+02 C 6468 BOND = 1440.2601 ANGLE = 3714.8908 DIHED = 5445.1475 VDWAALS = -3948.1504 EEL = -34972.0712 EGB = -7697.0873 1-4 VDW = 1809.2470 1-4 EEL = 23319.2011 RESTRAINT = 0.0000 ESURF = 182.9861 minimization completed, ENE= -.10705576E+05 RMS= 0.173917E+02 minimizing coord set # 37 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0774E+04 1.7360E+01 1.0659E+02 C 3427 BOND = 1460.3619 ANGLE = 3746.8051 DIHED = 5399.4824 VDWAALS = -3922.3961 EEL = -34836.7661 EGB = -7819.1166 1-4 VDW = 1774.4242 1-4 EEL = 23238.8348 RESTRAINT = 0.0000 ESURF = 184.2813 minimization completed, ENE= -.10774089E+05 RMS= 0.173602E+02 minimizing coord set # 38 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0782E+04 1.7326E+01 1.0427E+02 C 6301 BOND = 1434.2464 ANGLE = 3780.9033 DIHED = 5404.4549 VDWAALS = -3922.1960 EEL = -34850.8973 EGB = -7817.2192 1-4 VDW = 1764.7665 1-4 EEL = 23238.9208 RESTRAINT = 0.0000 ESURF = 185.3598 minimization completed, ENE= -.10781661E+05 RMS= 0.173264E+02 minimizing coord set # 39 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0634E+04 1.7306E+01 1.1239E+02 CG 2429 BOND = 1444.5238 ANGLE = 3760.9074 DIHED = 5455.8008 VDWAALS = -3918.2111 EEL = -34760.8384 EGB = -7837.2894 1-4 VDW = 1795.3414 1-4 EEL = 23240.0345 RESTRAINT = 0.0000 ESURF = 185.7591 minimization completed, ENE= -.10633972E+05 RMS= 0.173055E+02 minimizing coord set # 40 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0686E+04 1.7362E+01 1.2276E+02 C 2823 BOND = 1437.7946 ANGLE = 3807.8456 DIHED = 5369.9224 VDWAALS = -3960.8387 EEL = -34700.6634 EGB = -7955.4094 1-4 VDW = 1809.6972 1-4 EEL = 23320.6537 RESTRAINT = 0.0000 ESURF = 185.2528 minimization completed, ENE= -.10685745E+05 RMS= 0.173617E+02 minimizing coord set # 41 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0705E+04 1.7474E+01 1.4932E+02 C 1251 BOND = 1472.9322 ANGLE = 3714.6688 DIHED = 5413.9458 VDWAALS = -3900.4588 EEL = -34796.6997 EGB = -7807.4043 1-4 VDW = 1793.0949 1-4 EEL = 23218.9444 RESTRAINT = 0.0000 ESURF = 186.4466 minimization completed, ENE= -.10704530E+05 RMS= 0.174737E+02 minimizing coord set # 42 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0641E+04 1.7240E+01 1.1137E+02 N 2558 BOND = 1418.9835 ANGLE = 3790.5098 DIHED = 5447.3980 VDWAALS = -3873.0534 EEL = -34827.4633 EGB = -7826.1101 1-4 VDW = 1792.5731 1-4 EEL = 23250.1948 RESTRAINT = 0.0000 ESURF = 186.3308 minimization completed, ENE= -.10640637E+05 RMS= 0.172403E+02 minimizing coord set # 43 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0775E+04 1.7158E+01 1.0379E+02 C 4435 BOND = 1396.7580 ANGLE = 3796.1707 DIHED = 5384.1527 VDWAALS = -3938.9209 EEL = -34956.7187 EGB = -7762.2743 1-4 VDW = 1812.6227 1-4 EEL = 23308.8980 RESTRAINT = 0.0000 ESURF = 184.1773 minimization completed, ENE= -.10775134E+05 RMS= 0.171584E+02 minimizing coord set # 44 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0680E+04 1.7345E+01 1.1705E+02 C 2393 BOND = 1427.6006 ANGLE = 3804.5900 DIHED = 5421.3098 VDWAALS = -3908.8310 EEL = -34907.0936 EGB = -7778.3658 1-4 VDW = 1787.1672 1-4 EEL = 23289.4180 RESTRAINT = 0.0000 ESURF = 184.5591 minimization completed, ENE= -.10679646E+05 RMS= 0.173452E+02 minimizing coord set # 45 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0690E+04 1.7385E+01 1.2734E+02 C 7264 BOND = 1346.4461 ANGLE = 3849.3372 DIHED = 5474.7557 VDWAALS = -3947.3701 EEL = -34955.9535 EGB = -7748.5982 1-4 VDW = 1823.4530 1-4 EEL = 23285.4523 RESTRAINT = 0.0000 ESURF = 182.2040 minimization completed, ENE= -.10690273E+05 RMS= 0.173853E+02 minimizing coord set # 46 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0716E+04 1.7273E+01 1.3167E+02 CG 617 BOND = 1393.6071 ANGLE = 3699.2768 DIHED = 5445.5535 VDWAALS = -3889.3312 EEL = -34863.6968 EGB = -7803.1064 1-4 VDW = 1804.2953 1-4 EEL = 23313.2978 RESTRAINT = 0.0000 ESURF = 184.0516 minimization completed, ENE= -.10716052E+05 RMS= 0.172727E+02 minimizing coord set # 47 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0765E+04 1.7323E+01 1.1490E+02 C 436 BOND = 1421.6917 ANGLE = 3748.4845 DIHED = 5432.7482 VDWAALS = -3995.7694 EEL = -34897.1143 EGB = -7874.7257 1-4 VDW = 1828.9448 1-4 EEL = 23386.0284 RESTRAINT = 0.0000 ESURF = 184.4443 minimization completed, ENE= -.10765268E+05 RMS= 0.173235E+02 minimizing coord set # 48 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0731E+04 1.7375E+01 1.0682E+02 C 4082 BOND = 1447.4606 ANGLE = 3765.1945 DIHED = 5421.7688 VDWAALS = -3896.9375 EEL = -34813.0057 EGB = -7881.6653 1-4 VDW = 1768.6172 1-4 EEL = 23271.9580 RESTRAINT = 0.0000 ESURF = 185.2057 minimization completed, ENE= -.10731404E+05 RMS= 0.173754E+02 minimizing coord set # 49 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0677E+04 1.7311E+01 1.2738E+02 C 3459 BOND = 1394.2999 ANGLE = 3768.7603 DIHED = 5448.1056 VDWAALS = -3876.3427 EEL = -34899.4960 EGB = -7856.9723 1-4 VDW = 1813.2295 1-4 EEL = 23346.0658 RESTRAINT = 0.0000 ESURF = 185.3462 minimization completed, ENE= -.10677004E+05 RMS= 0.173109E+02 minimizing coord set # 50 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0705E+04 1.7267E+01 1.1748E+02 C 4907 BOND = 1413.5354 ANGLE = 3712.4305 DIHED = 5437.8969 VDWAALS = -3874.4495 EEL = -34939.2671 EGB = -7761.6096 1-4 VDW = 1816.4154 1-4 EEL = 23304.2857 RESTRAINT = 0.0000 ESURF = 185.3208 minimization completed, ENE= -.10705442E+05 RMS= 0.172671E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 698.36 ( 7.46% of Gen B) | Calc gb diag 5550.07 (59.32% of Gen B) | Calc gb off-diag 3107.74 (33.22% of Gen B) | Gen Born time 9356.18 (100.0% of Nonbo) | Nonbond force 9356.18 (100.0% of Force) | Bond/Angle/Dihedral 6.76 ( 0.07% of Force) | Force time 9362.95 (100.0% of Runmd) | Runmd Time 9362.95 (98.98% of Total) | Other 96.63 ( 1.02% of Total) | Total time 9459.63 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 19:12:36.556 on 10/19/2010 | Setup done at 19:12:37.121 on 10/19/2010 | Run done at 21:50:16.187 on 10/19/2010 | wallclock() was called 1809 times