------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 06/25/2009 at 07:23:53 [-O]verwriting output File Assignments: | MDIN: testenergy.sander.in | MDOUT: ligand-testenergy.sander.out |INPCRD: ligand-minimized.crd | PARM: ligand.prmtop |RESTRT: ligand-testenergy.crd | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Single-point energy evaluation &cntrl nstlim = 0, dt=0.002, ntb=0, igb=2, cut=999.0, rgbmax=999.0, ntt=3, tempi=300.0, temp0=300., gamma_ln=95., ntc=2, ntf=2, tol=0.00000001, &end -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 06/25/09 Time = 06:55:51 NATOM = 18 NTYPES = 4 NBONH = 10 MBONA = 8 NTHETH = 20 MTHETA = 10 NPHIH = 30 MPHIA = 12 NHPARM = 0 NPARM = 0 NNB = 85 NRES = 1 NBONA = 8 NTHETA = 10 NPHIA = 12 NUMBND = 4 NUMANG = 5 NPTRA = 3 NATYP = 4 NPHB = 0 IFBOX = 0 NMXRS = 18 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are H(N)-modified Bondi radii (mbondi2) | Memory Use Allocated | Real 1047 | Hollerith 111 | Integer 20774 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 89 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- TMP General flags: imin = 0, 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 = 2, ntb = 0, igb = 2, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 0.80000 gbbeta = 0.00000, gbgamma = 2.90912, surften = 0.00500 rdt = 0.00000, rgbmax = 999.00000 alpb = 0 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 0, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 71277 temp0 = 300.00000, tempi = 300.00000, gamma_ln= 95.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00000 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- TMP begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 408.15 PRESS = 0.0 Etot = 13.4895 EKtot = 17.8435 EPtot = -4.3539 BOND = 0.2231 ANGLE = 0.0842 DIHED = 0.0018 1-4 NB = 4.4957 1-4 EEL = -8.0674 VDWAALS = -0.5186 EELEC = 3.3411 EGB = -3.9138 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.00 ( 8.50% of Total) | Fast Water setup 0.00 ( 0.32% of Total) | Calc gb radii 0.00 (36.96% of Gen B) | Calc gb diag 0.00 (33.69% of Gen B) | Calc gb off-diag 0.00 (26.63% of Gen B) | Other 0.00 ( 2.72% of Gen B) | Gen Born time 0.00 (100.0% of Nonbo) | Nonbond force 0.00 (62.16% of Force) | Bond/Angle/Dihedral 0.00 (35.48% of Force) | Other 0.00 ( 2.36% of Force) | Force time 0.00 (45.19% of Runmd) | Other 0.00 (54.81% of Runmd) | Runmd Time 0.00 (17.35% of Total) | Other 0.00 (73.83% of Total) | Total time 0.00 (97.80% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 07:23:53.875 on 06/25/2009 | Setup done at 07:23:53.878 on 06/25/2009 | Run done at 07:23:53.879 on 06/25/2009 | wallclock() was called 28 times