------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 04/12/2005 at 11:06:00 [-O]verwriting output File Assignments: | MDIN: sanmin_lig.in | MDOUT: sanmin_lig.1.out |INPCRD: ../01_GenerateSnapshots/ras_raf_II_wt_lig.crd.1 | PARM: ../raf_wt.prmtop |RESTRT: sanmin_lig.1.restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: File generated by mm_pbsa.pl &cntrl ntxo = 0, ntf = 1, ntb = 0, dielc = 4, cut = 99.0, nsnb = 99999, scnb = 2.0, scee = 1.2, imin = 1, maxcyc = 100, ncyc = 0, drms = 0.1 &end &ewald eedmeth= 5, &end -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation | *** cutoff > system size, list only builds once |Largest sphere to fit in unit cell has radius = 45.585 | New format PARM file being parsed. | Version = 1.000 Date = 01/07/02 Time = 15:05:50 NATOM = 1241 NTYPES = 14 NBONH = 633 MBONA = 617 NTHETH = 1437 MTHETA = 830 NPHIH = 2560 MPHIA = 1442 NHPARM = 0 NPARM = 0 NNB = 6843 NRES = 76 NBONA = 617 NTHETA = 830 NPHIA = 1442 NUMBND = 42 NUMANG = 92 NPTRA = 33 NATYP = 29 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 98042 | Hollerith 7524 | Integer 1719730 | Max Pairs 769420 | Max Rstack 62410 | Max Istack 6205 | Total 11030 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 = 0, 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 = 99999 ipol = 0, gbsa = 0, iesp = 0 dielc = 4.00000, cut = 99.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 100, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.10000 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- CARNAL dump begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 Sum of charges from parm topology file = 2.99999999 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- eedmeth=5: Using 1/r dielectric --------------------------------------------------- | Local SIZE OF NONBOND LIST = 762643 | TOTAL SIZE OF NONBOND LIST = 762643 NSTEP ENERGY RMS GMAX NAME NUMBER 1 7.4451E+02 1.6716E+01 9.1529E+01 C 1030 BOND = 209.7898 ANGLE = 612.1167 DIHED = 454.5684 VDWAALS = -546.2276 EEL = -414.5321 HBOND = 0.0000 1-4 VDW = 257.2640 1-4 EEL = 171.5283 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 50 -8.1868E+01 1.2519E+00 1.2837E+01 CE2 980 BOND = 25.1971 ANGLE = 153.5074 DIHED = 340.5061 VDWAALS = -615.9481 EEL = -417.0840 HBOND = 0.0000 1-4 VDW = 235.2911 1-4 EEL = 196.6627 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -1.2587E+02 7.1338E-01 6.0757E+00 CD1 976 BOND = 22.2594 ANGLE = 139.4366 DIHED = 322.6181 VDWAALS = -629.2903 EEL = -415.9974 HBOND = 0.0000 1-4 VDW = 237.2821 1-4 EEL = 197.8230 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 100 -1.2587E+02 7.1338E-01 6.0757E+00 CD1 976 BOND = 22.2594 ANGLE = 139.4366 DIHED = 322.6181 VDWAALS = -629.2903 EEL = -415.9974 HBOND = 0.0000 1-4 VDW = 237.2821 1-4 EEL = 197.8230 RESTRAINT = 0.0000 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.01 ( 0.08% of Total) | Build the list 0.22 (90.73% of List ) | Other 0.02 ( 9.27% of List ) | List time 0.24 ( 1.71% of Nonbo) | Short_ene time 13.50 (99.65% of Direc) | Other 0.05 ( 0.35% of Direc) | Direct Ewald time 13.55 (98.95% of Ewald) | Force Adjust 0.13 ( 0.98% of Ewald) | Virial junk 0.01 ( 0.06% of Ewald) | Start sycnronization 0.00 ( 0.01% of Ewald) | Other 0.00 ( 0.01% of Ewald) | Ewald time 13.69 (98.29% of Nonbo) | Nonbond force 13.93 (95.94% of Force) | Bond/Angle/Dihedral 0.59 ( 4.04% of Force) | Other 0.00 ( 0.02% of Force) | Force time 14.52 (100.0% of Runmd) | Runmd Time 14.52 (98.60% of Total) | Other 0.19 ( 1.31% of Total) | Total time 14.72 (100.0% of ALL ) | Highest rstack allocated: 17465 | Highest istack allocated: 1232 | Job began at 11:06:00.536 on 04/12/2005 | Setup done at 11:06:00.685 on 04/12/2005 | Run done at 11:06:15.260 on 04/12/2005 | wallclock() was called 1810 times