------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 02/16/2011 at 03:29:59 [-O]verwriting output File Assignments: | MDIN: _MMPBSA_pb.mdin | MDOUT: _MMPBSA_complex_pb.mdout |INPCRD: _MMPBSA_dummycomplex.inpcrd | PARM: ../com.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _MMPBSA_complex.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 = 12/19/10 Time = 21:43:59 NATOM = 10605 NTYPES = 15 NBONH = 5371 MBONA = 5360 NTHETH = 12201 MTHETA = 7274 NPHIH = 22860 MPHIA = 18057 NHPARM = 0 NPARM = 0 NNB = 58736 NRES = 661 NBONA = 5360 NTHETA = 7274 NPHIA = 18057 NUMBND = 43 NUMANG = 91 NPTRA = 43 NATYP = 30 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 711284 | Hollerith 32478 | Integer 570608 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 7912 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