------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 02/15/2011 at 23:11:06 [-O]verwriting output File Assignments: | MDIN: _MMPBSA_pb.mdin | MDOUT: _MMPBSA_ligand_pb.mdout |INPCRD: _MMPBSA_dummyligand.inpcrd | PARM: ../lig.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _MMPBSA_ligand.mdcrd | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, cut=999.0, ntpr=1, imin=5, maxcyc=0, igb=10, ipb=1, inp=1, / &pb dbfopt=1, epsin=1, epsout=80, istrng=100.0, radiopt=0, sprob=1.4, space=0.5, maxitn=1000, cavity_surften=0.00542, cavity_offset=-1.008, fillratio=4, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: PB Info in pb_read(): npopt has been overwritten with inp | New format PARM file being parsed. | Version = 1.000 Date = 02/15/11 Time = 19:27:49 NATOM = 1 NTYPES = 1 NBONH = 0 MBONA = 0 NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0 NHPARM = 0 NPARM = 0 NNB = 1 NRES = 1 NBONA = 0 NTHETA = 0 NPHIA = 0 NUMBND = 0 NUMANG = 0 NPTRA = 0 NATYP = 1 NPHB = 0 IFBOX = 0 NMXRS = 1 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 197 | Hollerith 6 | Integer 20018 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 79 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 = 1, 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 = 10, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 10, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- trajectory generated by ptraj 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 Total surface charge -1.9751 Reaction field energy -437.2144 Cavity solvation energy -0.4352 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.3765E+02 0.0000E+00 0.0000E+00 MG 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EPB = -437.2124 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ECAVITY = -0.4352 EDISPER = 0.0000 minimization completed, ENE= -.43764764E+03 RMS= 0.000000E+00 minimizing coord set # 2 Total surface charge -1.9751 Reaction field energy -437.2137 Cavity solvation energy -0.4352 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.3765E+02 0.0000E+00 0.0000E+00 MG 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EPB = -437.2133 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ECAVITY = -0.4352 EDISPER = 0.0000 minimization completed, ENE= -.43764851E+03 RMS= 0.000000E+00 minimizing coord set # 3 Total surface charge -1.9751 Reaction field energy -437.2153 Cavity solvation energy -0.4352 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.3765E+02 0.0000E+00 0.0000E+00 MG 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EPB = -437.2128 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ECAVITY = -0.4352 EDISPER = 0.0000 minimization completed, ENE= -.43764799E+03 RMS= 0.000000E+00 minimizing coord set # 4 Total surface charge -1.9751 Reaction field energy -437.2153 Cavity solvation energy -0.4352 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.3765E+02 0.0000E+00 0.0000E+00 MG 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EPB = -437.2128 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ECAVITY = -0.4352 EDISPER = 0.0000 minimization completed, ENE= -.43764801E+03 RMS= 0.000000E+00 minimizing coord set # 5 Total surface charge -1.9751 Reaction field energy -437.2138 Cavity solvation energy -0.4352 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.3765E+02 0.0000E+00 0.0000E+00 MG 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EPB = -437.2135 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ECAVITY = -0.4352 EDISPER = 0.0000 minimization completed, ENE= -.43764871E+03 RMS= 0.000000E+00 minimizing coord set # 6 Total surface charge -1.9751 Reaction field energy -437.2141 Cavity solvation energy -0.4352 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.3765E+02 0.0000E+00 0.0000E+00 MG 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EPB = -437.2132 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ECAVITY = -0.4352 EDISPER = 0.0000 minimization completed, ENE= -.43764836E+03 RMS= 0.000000E+00 minimizing coord set # 7 Total surface charge -1.9751 Reaction field energy -437.2158 Cavity solvation energy -0.4352 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.3765E+02 0.0000E+00 0.0000E+00 MG 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EPB = -437.2125 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ECAVITY = -0.4352 EDISPER = 0.0000 minimization completed, ENE= -.43764771E+03 RMS= 0.000000E+00 minimizing coord set # 8 Total surface charge -1.9751 Reaction field energy -437.2158 Cavity solvation energy -0.4352 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.3765E+02 0.0000E+00 0.0000E+00 MG 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EPB = -437.2127 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ECAVITY = -0.4352 EDISPER = 0.0000 minimization completed, ENE= -.43764793E+03 RMS= 0.000000E+00 minimizing coord set # 9 Total surface charge -1.9751 Reaction field energy -437.2173 Cavity solvation energy -0.4352 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.3765E+02 0.0000E+00 0.0000E+00 MG 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EPB = -437.2122 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ECAVITY = -0.4352 EDISPER = 0.0000 minimization completed, ENE= -.43764735E+03 RMS= 0.000000E+00 minimizing coord set # 10 Total surface charge -1.9751 Reaction field energy -437.2152 Cavity solvation energy -0.4352 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.3765E+02 0.0000E+00 0.0000E+00 MG 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EPB = -437.2128 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ECAVITY = -0.4352 EDISPER = 0.0000 minimization completed, ENE= -.43764798E+03 RMS= 0.000000E+00 minimizing coord set # 11 Total surface charge -1.9751 Reaction field energy -437.2156 Cavity solvation energy -0.4352 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.3765E+02 0.0000E+00 0.0000E+00 MG 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EPB = -437.2127 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ECAVITY = -0.4352 EDISPER = 0.0000 minimization completed, ENE= -.43764787E+03 RMS= 0.000000E+00 minimizing coord set # 12 Total surface charge -1.9751 Reaction field energy -437.2158 Cavity solvation energy -0.4352 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.3765E+02 0.0000E+00 0.0000E+00 MG 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EPB = -437.2126 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ECAVITY = -0.4352 EDISPER = 0.0000 minimization completed, ENE= -.43764781E+03 RMS= 0.000000E+00 minimizing coord set # 13 Total surface charge -1.9751 Reaction field energy -437.2163 Cavity solvation energy -0.4352 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.3765E+02 0.0000E+00 0.0000E+00 MG 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EPB = -437.2125 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ECAVITY = -0.4352 EDISPER = 0.0000 minimization completed, ENE= -.43764770E+03 RMS= 0.000000E+00 minimizing coord set # 14 Total surface charge -1.9751 Reaction field energy -437.2152 Cavity solvation energy -0.4352 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.3765E+02 0.0000E+00 0.0000E+00 MG 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EPB = -437.2128 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ECAVITY = -0.4352 EDISPER = 0.0000 minimization completed, ENE= -.43764804E+03 RMS= 0.000000E+00 minimizing coord set # 15 Total surface charge -1.9751 Reaction field energy -437.2163 Cavity solvation energy -0.4352 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.3765E+02 0.0000E+00 0.0000E+00 MG 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EPB = -437.2126 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ECAVITY = -0.4352 EDISPER = 0.0000 minimization completed, ENE= -.43764779E+03 RMS= 0.000000E+00 minimizing coord set # 16 Total surface charge -1.9751 Reaction field energy -437.2170 Cavity solvation energy -0.4352 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.3765E+02 0.0000E+00 0.0000E+00 MG 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EPB = -437.2125 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ECAVITY = -0.4352 EDISPER = 0.0000 minimization completed, ENE= -.43764768E+03 RMS= 0.000000E+00 minimizing coord set # 17 Total surface charge -1.9751 Reaction field energy -437.2150 Cavity solvation energy -0.4352 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.3765E+02 0.0000E+00 0.0000E+00 MG 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EPB = -437.2130 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ECAVITY = -0.4352 EDISPER = 0.0000 minimization completed, ENE= -.43764822E+03 RMS= 0.000000E+00 minimizing coord set # 18 Total surface charge -1.9751 Reaction field energy -437.2153 Cavity solvation energy -0.4352 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.3765E+02 0.0000E+00 0.0000E+00 MG 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EPB = -437.2128 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ECAVITY = -0.4352 EDISPER = 0.0000 minimization completed, ENE= -.43764802E+03 RMS= 0.000000E+00 minimizing coord set # 19 Total surface charge -1.9751 Reaction field energy -437.2172 Cavity solvation energy -0.4352 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.3765E+02 0.0000E+00 0.0000E+00 MG 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EPB = -437.2120 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ECAVITY = -0.4352 EDISPER = 0.0000 minimization completed, ENE= -.43764718E+03 RMS= 0.000000E+00 minimizing coord set # 20 Total surface charge -1.9751 Reaction field energy -437.2161 Cavity solvation energy -0.4352 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.3765E+02 0.0000E+00 0.0000E+00 MG 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 EPB = -437.2125 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ECAVITY = -0.4352 EDISPER = 0.0000 minimization completed, ENE= -.43764774E+03 RMS= 0.000000E+00 TRAJENE: Trajectory file ended TRAJENE: Trajene complete. -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.00 ( 0.04% of Total) | PB Nonbond 0.40 (100.0% of Nonbo) | NP Nonbond 0.00 ( 0.04% of Nonbo) | IPS excludes 0.00 ( 0.01% of Nonbo) | Nonbond force 0.40 (99.87% of Force) | Bond/Angle/Dihedral 0.00 ( 0.04% of Force) | Other 0.00 ( 0.10% of Force) | Force time 0.40 (100.0% of Runmd) | Runmd Time 0.40 (98.06% of Total) | Other 0.01 ( 1.90% of Total) | Total time 0.41 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 23:11:06.314 on 02/15/2011 | Setup done at 23:11:06.316 on 02/15/2011 | Run done at 23:11:06.720 on 02/15/2011 | wallclock() was called 489 times