------------------------------------------------------- Amber 7 SANDER Scripps/UCSF 2002 ------------------------------------------------------- | Wed Jul 7 11:19:35 2004 [-O]verwriting output File Assignments: | MDIN: p2Im.in | MDOUT: diarga.out |INPCRD: diarg.crd | PARM: diarg.top |RESTRT: diargmin.crd | REFC: diarg.crd | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: #minimisation 2 #25kcal on protein &cntrl imin=1, ntx=1,ntb=0, ntr=0,dielc=4,cut=300, maxcyc=1000, ncyc=500, &end &ewald use_pme=0, eedmeth=5, &end -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: MEM_ALLOC | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation | *** cutoff > system size, list only builds once | New format PARM file being parsed. | Version = 1.000 Date = 07/06/04 Time = 20:55:50 NATOM = 51 NTYPES = 8 NBONH = 28 MBONA = 22 NTHETH = 60 MTHETA = 27 NPHIH = 103 MPHIA = 38 NHPARM = 0 NPARM = 0 NNB = 261 NRES = 2 NBONA = 22 NTHETA = 27 NPHIA = 38 NUMBND = 15 NUMANG = 32 NPTRA = 21 NATYP = 12 NPHB = 0 IFBOX = 0 NMXRS = 26 IFCAP = 0 NEXTRA = 0 | Memory Use Allocated | Real 5219 | Hollerith 310 | Integer 533696 | Max Pairs 1275 | Max Rstack 7000000 | Max Istack 2000000 | 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 dielc = 4.00000, cut = 300.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 1000, ncyc = 500, ntmin = 1 dx0 = 0.01000, dxm = 0.50000, 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 Sum of charges from parm topology file = 1.00000000 Assuming uniform neutralizing plasma -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- eedmeth=5: Using 1/r dielectric --------------------------------------------------- | Local SIZE OF NONBOND LIST = 1017 | TOTAL SIZE OF NONBOND LIST = 1017 NSTEP ENERGY RMS GMAX NAME NUMBER 1 1.2759E+02 7.9611E+01 4.7083E+02 HG2 11 BOND = 1.2756 ANGLE = 4.4522 DIHED = 5.5100 VDWAALS = 136.5059 EEL = 9.7190 HBOND = 0.0000 1-4 VDW = 10.5377 1-4 EEL = -40.4090 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 50 -1.1258E+01 3.5221E+00 2.3890E+01 C 25 BOND = 0.9902 ANGLE = 4.2883 DIHED = 5.8526 VDWAALS = 0.2682 EEL = 9.0285 HBOND = 0.0000 1-4 VDW = 8.5426 1-4 EEL = -40.2286 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -1.5454E+01 2.6577E+00 1.4685E+01 C 49 BOND = 0.7300 ANGLE = 3.2956 DIHED = 5.8273 VDWAALS = -1.9402 EEL = 9.2276 HBOND = 0.0000 1-4 VDW = 7.5479 1-4 EEL = -40.1427 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 150 -1.7303E+01 1.2388E+00 8.4160E+00 C 25 BOND = 0.5136 ANGLE = 2.9379 DIHED = 5.8577 VDWAALS = -2.7956 EEL = 9.3947 HBOND = 0.0000 1-4 VDW = 6.9899 1-4 EEL = -40.2007 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -1.8269E+01 7.3430E-01 4.4267E+00 C 25 BOND = 0.4742 ANGLE = 2.6697 DIHED = 5.8974 VDWAALS = -3.3486 EEL = 9.5616 HBOND = 0.0000 1-4 VDW = 6.6779 1-4 EEL = -40.2017 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 250 -1.8875E+01 3.6993E-01 1.8580E+00 C 25 BOND = 0.4507 ANGLE = 2.5190 DIHED = 5.9241 VDWAALS = -3.6875 EEL = 9.6959 HBOND = 0.0000 1-4 VDW = 6.4487 1-4 EEL = -40.2259 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 300 -1.9255E+01 6.5576E-01 4.2104E+00 C 25 BOND = 0.4490 ANGLE = 2.4133 DIHED = 5.9408 VDWAALS = -3.9196 EEL = 9.8132 HBOND = 0.0000 1-4 VDW = 6.2888 1-4 EEL = -40.2406 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 350 -1.9511E+01 3.1263E-01 2.0770E+00 C 49 BOND = 0.4390 ANGLE = 2.3292 DIHED = 5.9499 VDWAALS = -4.0768 EEL = 9.9080 HBOND = 0.0000 1-4 VDW = 6.1842 1-4 EEL = -40.2450 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 400 -1.9689E+01 7.2612E-01 5.8901E+00 C 49 BOND = 0.4394 ANGLE = 2.2740 DIHED = 5.9501 VDWAALS = -4.1897 EEL = 9.9904 HBOND = 0.0000 1-4 VDW = 6.0983 1-4 EEL = -40.2515 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 450 -1.9848E+01 4.3334E-01 3.2236E+00 C 49 BOND = 0.4444 ANGLE = 2.2200 DIHED = 5.9478 VDWAALS = -4.2781 EEL = 10.0616 HBOND = 0.0000 1-4 VDW = 6.0208 1-4 EEL = -40.2643 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 500 -1.9968E+01 6.3472E-01 4.9012E+00 C 49 BOND = 0.4489 ANGLE = 2.1800 DIHED = 5.9396 VDWAALS = -4.3480 EEL = 10.1280 HBOND = 0.0000 1-4 VDW = 5.9563 1-4 EEL = -40.2724 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 550 -2.1356E+01 1.7357E+00 9.4841E+00 C 25 BOND = 0.4540 ANGLE = 2.2076 DIHED = 4.5035 VDWAALS = -4.4835 EEL = 10.9495 HBOND = 0.0000 1-4 VDW = 5.2889 1-4 EEL = -40.2765 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 600 -2.2980E+01 8.1443E-01 3.9838E+00 C 49 BOND = 0.4023 ANGLE = 1.9902 DIHED = 3.2437 VDWAALS = -4.6110 EEL = 11.1570 HBOND = 0.0000 1-4 VDW = 5.1319 1-4 EEL = -40.2942 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 650 -2.3565E+01 2.6592E-01 9.1463E-01 H 28 BOND = 0.4038 ANGLE = 1.8290 DIHED = 2.8791 VDWAALS = -4.6897 EEL = 11.2377 HBOND = 0.0000 1-4 VDW = 5.1668 1-4 EEL = -40.3917 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 700 -2.3713E+01 1.6764E-01 6.2181E-01 CZ 18 BOND = 0.4076 ANGLE = 1.7857 DIHED = 2.8442 VDWAALS = -4.7599 EEL = 11.2556 HBOND = 0.0000 1-4 VDW = 5.1777 1-4 EEL = -40.4243 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 750 -2.3751E+01 1.6471E-01 6.2852E-01 C 25 BOND = 0.4148 ANGLE = 1.7507 DIHED = 2.8486 VDWAALS = -4.7833 EEL = 11.2651 HBOND = 0.0000 1-4 VDW = 5.1799 1-4 EEL = -40.4264 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 800 -2.3774E+01 1.2439E-01 4.0155E-01 CZ 18 BOND = 0.4091 ANGLE = 1.7419 DIHED = 2.8398 VDWAALS = -4.7928 EEL = 11.2782 HBOND = 0.0000 1-4 VDW = 5.1776 1-4 EEL = -40.4279 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 850 -2.3796E+01 1.3785E-01 6.6480E-01 C 49 BOND = 0.4127 ANGLE = 1.7244 DIHED = 2.8318 VDWAALS = -4.8029 EEL = 11.2944 HBOND = 0.0000 1-4 VDW = 5.1710 1-4 EEL = -40.4278 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 900 -2.3814E+01 8.8792E-02 2.8868E-01 N 27 BOND = 0.4067 ANGLE = 1.7211 DIHED = 2.8197 VDWAALS = -4.8070 EEL = 11.3072 HBOND = 0.0000 1-4 VDW = 5.1653 1-4 EEL = -40.4267 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 950 -2.3830E+01 8.1610E-02 2.9258E-01 HA 30 BOND = 0.4059 ANGLE = 1.7113 DIHED = 2.8106 VDWAALS = -4.8129 EEL = 11.3196 HBOND = 0.0000 1-4 VDW = 5.1623 1-4 EEL = -40.4264 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1000 -2.3844E+01 7.7895E-02 2.7645E-01 N 27 BOND = 0.4048 ANGLE = 1.7031 DIHED = 2.8022 VDWAALS = -4.8180 EEL = 11.3314 HBOND = 0.0000 1-4 VDW = 5.1589 1-4 EEL = -40.4264 RESTRAINT = 0.0000 MAXIMUM NUMBER OF F EVALUATION EXCEEDED FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1000 -2.3844E+01 7.7895E-02 2.7645E-01 N 27 BOND = 0.4048 ANGLE = 1.7031 DIHED = 2.8022 VDWAALS = -4.8180 EEL = 11.3314 HBOND = 0.0000 1-4 VDW = 5.1589 1-4 EEL = -40.4264 RESTRAINT = 0.0000 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Direct Ewald time 0.41 (87.23% of Ewald) | Finish NB virial 0.01 ( 2.13% of Ewald) | Other 0.05 (10.64% of Ewald) | Ewald time 0.47 (100.0% of Nonbo) | Nonbond force 0.47 (57.32% of Force) | Angle energy 0.09 (10.98% of Force) | Dihedral energy 0.24 (29.27% of Force) | Other 0.02 ( 2.44% of Force) | Force time 0.82 (100.0% of Runmd) | Runmd Time 0.82 (97.62% of Total) | Other 0.02 ( 2.38% of Total) | Total time 0.84 (100.0% of ALL ) | Highest rstack allocated: 225 | Highest istack allocated: 2822 | Setup wallclock 0 seconds | Nonsetup wallclock 2 seconds