------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | Run on 06/06/2010 at 14:48:47 [-O]verwriting output File Assignments: | MDIN: _MMPBSA_pb.mdin | MDOUT: _MMPBSA_complex_pb.mdout |INPCRD: _MMPBSA_dummycomplex.inpcrd | PARM: 2PRG_rosi_NW.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _MMPBSA_complex.mdcrd | Here is the input file: File generated by MMPBSA.py &cntrl ntb=0, cut=999.0, nsnb=99999, imin=5, maxcyc=0, cutcap=-1, xcap=0, ycap=0, zcap=0, idecomp=0, ntpr=1, ivcap=0, ntmin=2, igb=10, &pb dbfopt=1, epsin=1, epsout=80, istrng=100.0, radiopt=0, sprob=1.4, space=0.5, maxitn=1000, npopt=1 cavity_surften=0.00542, cavity_offset=-1.008, fillratio=4, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 06/01/10 Time = 15:29:54 NATOM = 4682 NTYPES = 15 NBONH = 2376 MBONA = 2346 NTHETH = 5431 MTHETA = 3163 NPHIH = 10160 MPHIA = 7918 NHPARM = 0 NPARM = 0 NNB = 25948 NRES = 285 NBONA = 2346 NTHETA = 3163 NPHIA = 7918 NUMBND = 52 NUMANG = 106 NPTRA = 45 NATYP = 39 NPHB = 0 IFBOX = 0 NMXRS = 44 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 300139 | Hollerith 28379 | Integer 263209 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 3483 kbytes | 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 = 99999 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 10, ntmin = 2 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 SA Bomb in sa_arc(): Allocation aborted 0 210 210 0 0