------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 08/17/2004 at 15:03:15 [-O]verwriting output File Assignments: | MDIN: min_qmmm.in | MDOUT: min_qmmm.out |INPCRD: NMA.inpcrd | PARM: NMA.prmtop |RESTRT: NMA_min_qmmm.crd | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Initial min of our structure QMMM &cntrl imin=1, maxcyc=500, ncyc=200, cut=20, ntb=0, fcap=1.5, ifqt=1, nqt=12, idc=0, / 1 2 3 4 5 6 7 8 9 10 11 12 END END -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 08/13/04 Time = 16:17:36 NATOM = 1239 NTYPES = 9 NBONH = 1234 MBONA = 4 NTHETH = 14 MTHETA = 4 NPHIH = 21 MPHIA = 3 NHPARM = 0 NPARM = 0 NNB = 1682 NRES = 411 NBONA = 4 NTHETA = 4 NPHIA = 3 NUMBND = 9 NUMANG = 10 NPTRA = 7 NATYP = 9 NPHB = 1 IFBOX = 0 NMXRS = 6 IFCAP = 1 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 45854 | Hollerith 9347 | Integer 46683 | Max Pairs 766941 | Max Rstack 62390 | Max Istack 6195 | Total 4084 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 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 = 0, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 20.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 500, ncyc = 200, ntmin = 1 dx0 = 0.01000, drms = 0.00010 Water cap: ivcap = 0, natcap = 12 fcap = 1.50000, cutcap = 15.00000 xcap = 2.71135, ycap = 1.22332, zcap = -1.12736 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 409 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NB-update: NPAIRS = 635049 HBPAIR = 275700 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -3.1187E+03 1.1633E+01 6.4858E+01 N 7 BOND = 0.0197 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 403.8488 EEL = -3472.7798 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ESCF = -49.7927 NB-update: NPAIRS = 635679 HBPAIR = 275980 NB-update: NPAIRS = 635661 HBPAIR = 275972 NSTEP ENERGY RMS GMAX NAME NUMBER 50 -3.7738E+03 4.5603E+00 1.7053E+02 C 5 BOND = 205.1061 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 426.5365 EEL = -4367.1919 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ESCF = -38.2046 NB-update: NPAIRS = 636165 HBPAIR = 276196 NB-update: NPAIRS = 636525 HBPAIR = 276356 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -3.9412E+03 3.1769E+00 1.1733E+02 C 5 BOND = 223.6916 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 476.6928 EEL = -4593.5833 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ESCF = -47.9766 NB-update: NPAIRS = 636939 HBPAIR = 276540 NB-update: NPAIRS = 637245 HBPAIR = 276676 NSTEP ENERGY RMS GMAX NAME NUMBER 150 -4.0258E+03 1.9133E+00 6.6946E+01 C 5 BOND = 234.6365 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 514.6429 EEL = -4722.4322 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ESCF = -52.6262 NB-update: NPAIRS = 637650 HBPAIR = 276856 NB-update: NPAIRS = 637920 HBPAIR = 276976 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -4.0854E+03 7.8843E-01 1.4004E+01 C 5 BOND = 243.3085 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 547.7283 EEL = -4822.4019 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ESCF = -54.0663 NB-update: NPAIRS = 641556 HBPAIR = 278592 NB-update: NPAIRS = 643113 HBPAIR = 279284 NSTEP ENERGY RMS GMAX NAME NUMBER 250 -4.3448E+03 2.3892E+00 4.6222E+01 O 6 BOND = 297.4212 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 767.6264 EEL = -5356.2135 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ESCF = -53.6764 NB-update: NPAIRS = 644202 HBPAIR = 279768 NB-update: NPAIRS = 645570 HBPAIR = 280376 NSTEP ENERGY RMS GMAX NAME NUMBER 300 -4.4318E+03 1.3270E+00 2.2395E+01 HH31 10 BOND = 304.5031 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 821.9316 EEL = -5502.9905 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ESCF = -55.2632 NB-update: NPAIRS = 646380 HBPAIR = 280736 NB-update: NPAIRS = 647100 HBPAIR = 281056 NSTEP ENERGY RMS GMAX NAME NUMBER 350 -4.4990E+03 1.0887E+00 1.9034E+01 HH31 10 BOND = 318.3004 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 864.3982 EEL = -5624.7862 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ESCF = -56.8908 NB-update: NPAIRS = 648774 HBPAIR = 281800 NB-update: NPAIRS = 649431 HBPAIR = 282092 NSTEP ENERGY RMS GMAX NAME NUMBER 400 -4.5660E+03 1.0394E+00 2.5558E+01 CH3 9 BOND = 323.0300 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 913.8361 EEL = -5744.6332 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ESCF = -58.2641 NB-update: NPAIRS = 650664 HBPAIR = 282640 NB-update: NPAIRS = 651231 HBPAIR = 282892 NSTEP ENERGY RMS GMAX NAME NUMBER 450 -4.6125E+03 1.1075E+00 1.6358E+01 O 6 BOND = 332.5792 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 947.6493 EEL = -5832.9097 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ESCF = -59.8077 NB-update: NPAIRS = 652329 HBPAIR = 283380 NB-update: NPAIRS = 653004 HBPAIR = 283680 NSTEP ENERGY RMS GMAX NAME NUMBER 500 -4.6525E+03 6.0593E-01 7.7037E+00 C 5 BOND = 343.7006 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 982.1865 EEL = -5917.1502 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ESCF = -61.1920 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 500 -4.6525E+03 6.0593E-01 7.7037E+00 C 5 BOND = 343.7006 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 982.1865 EEL = -5917.1502 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ESCF = -61.1920 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.03 ( 0.03% of Total) | Nonbond force 18.51 (14.70% of Force) | QMMM energy 107.24 (85.19% of Force) | Bond/Angle/Dihedral 0.08 ( 0.07% of Force) | Other 0.05 ( 0.04% of Force) | Force time 125.89 (100.0% of Runmd) | Runmd Time 125.89 (99.57% of Total) | Other 0.51 ( 0.41% of Total) | Total time 126.44 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 15:03:15.657 on 08/17/2004 | Setup done at 15:03:15.900 on 08/17/2004 | Run done at 15:05:22.094 on 08/17/2004 | wallclock() was called 14454 times