------------------------------------------------------- PBSA VERSION 2009 UC Irvine ------------------------------------------------------- | Run on 02/18/2014 at 12:15:49 [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: mdout.tsrb.min |INPCRD: tsrb.rst | PARM: prmtop | Here is the input file: test of PB implicit solvent on 1tsr b-chain &cntrl ntx=1, imin=1, ipb=1, inp=1 / &pb npbverb=0, istrng=0, epsout=80.0, epsin=1.0, space=0.5, accept=0.001, radiopt=0, dprob=1.4, arcres=0.25, eneopt=2, bcopt=6, / PB Warning in pb_read(): sprob=0.557 is optimized for inp=2 and should not be used with inp=1. It has been reset to 1.4. PB Warning in pb_read(): cavity_surften=0.0378 is optimized for inp=2 and should not be used with inp=1. It has been reset to 0.005000. PB Warning in pb_read(): cavity_offset=-0.5692 is optimized for inp=2 and should not be used with inp=1. It has been reset to 0.000. -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 11/15/04 Time = 15:13:17 NATOM = 3010 NTYPES = 14 NBONH = 1486 MBONA = 1559 NTHETH = 3362 MTHETA = 2115 NPHIH = 6127 MPHIA = 2961 NHPARM = 0 NPARM = 0 NNB = 16582 NRES = 194 NBONA = 1559 NTHETA = 2115 NPHIA = 2961 NUMBND = 41 NUMANG = 89 NPTRA = 30 NATYP = 28 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 111516 | Hollerith 18256 | Integer 143139 | Max Pairs 1 | Max Rstack 1 | Max Istack 1 | Total 1501 kbytes -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 1, 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 = 1, ipb = 1, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 1, ncyc = 10, ntmin = 1 dx0 = 0.01000, drms = 0.00010 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- Total surface charge -2.9481 Reaction field energy -2432.8253 Cavity solvation energy 50.0651 NSTEP = 1 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -15823.3228 EKtot = 0.0000 EPtot = 0.0000 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = -1621.1656 EELEC = -11819.3970 EPB = -2432.8253 RESTRAINT = 0.0000 ECAVITY= 50.0651 EDISPER = 0.0000 ------------------------------------------------------------------------------ Maximum number of minimization cycles reached. FINAL RESULTS NSTEP = 1 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -15823.3228 EKtot = 0.0000 EPtot = 0.0000 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = -1621.1656 EELEC = -11819.3970 EPB = -2432.8253 RESTRAINT = 0.0000 ECAVITY= 50.0651 EDISPER = 0.0000 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Total time 43.72 | Read prm/crd time 0.05 | Force time 43.67 | Nonbond force 43.67 | PB Nonbond 43.67 | PB NB list 0.22 | PB FD grid 0.01 | PB Sasa 2.18 | PB FD force 40.94 | PB Set linear sys 1.10 | PB Solver 36.30 | PB Direct 0.32 | PB SA srf 0.11 | PB SA arc 2.07 | PB SA arc setup 0.01 | PB circle 1.71 | PB exclude 0.35 | PB exmol 1.09 | PB exmol setup 0.06 | PB exmol part a 0.01 | PB exmol part b 0.31 | PB exmol part c 0.08 | PB exmol part d 0.02 | PB exmol part e 0.15 | PB exmol part f 0.35 | PB epsbnd 0.02 | PB epsmap 0.09 | Job began at 12:15:49.881 on 02/18/2014 | Setup done at 12:15:49.933 on 02/18/2014 | Run done at 12:16:33.600 on 02/18/2014 | wallclock() was called 100 times