------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 06/18/2006 at 15:59:26 [-O]verwriting output File Assignments: | MDIN: thio_min.in | MDOUT: thio_min.out |INPCRD: thio_ash.inpcrd | PARM: thio_ash.prmtop |RESTRT: thio_ash_min.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: minimise thioredoxin &cntrl imin=1, maxcyc=500, ncyc=250, igb=5, ntb=0, ntf=2, ntc=2 ntpr=50, cut=999.0, rgbmax=999.0 / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 06/18/06 Time = 15:22:46 NATOM = 1655 NTYPES = 14 NBONH = 833 MBONA = 838 NTHETH = 1913 MTHETA = 1138 NPHIH = 3393 MPHIA = 2014 NHPARM = 0 NPARM = 0 NNB = 9202 NRES = 108 NBONA = 838 NTHETA = 1138 NPHIA = 2014 NUMBND = 39 NUMANG = 89 NPTRA = 33 NATYP = 25 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are H(N)-modified Bondi radii (mbondi2) | Memory Use Allocated | Real 106309 | Hollerith 10040 | Integer 101309 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 1265 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 = 2, ntb = 0, igb = 5, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, 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 Energy minimization: maxcyc = 500, ncyc = 250, ntmin = 1 dx0 = 0.01000, drms = 0.00010 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NSTEP ENERGY RMS GMAX NAME NUMBER 1 -2.9582E+03 1.5441E+01 1.6606E+02 HD3 1021 BOND = 156.6407 ANGLE = 324.4165 DIHED = 492.8692 VDWAALS = -735.8398 EEL = -8365.0098 EGB = -1477.8136 1-4 VDW = 487.4103 1-4 EEL = 6159.0838 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 50 -3.5669E+03 1.3831E+00 1.2675E+01 HZ1 282 BOND = 30.5282 ANGLE = 167.9499 DIHED = 485.6586 VDWAALS = -855.3265 EEL = -8277.3666 EGB = -1494.9850 1-4 VDW = 366.4979 1-4 EEL = 6010.1845 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -3.6052E+03 1.3120E+00 1.2843E+01 HZ1 282 BOND = 38.0039 ANGLE = 176.6813 DIHED = 484.3486 VDWAALS = -869.3773 EEL = -8248.8979 EGB = -1502.4594 1-4 VDW = 344.1327 1-4 EEL = 5972.3619 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 150 -3.6208E+03 1.4395E+00 2.1724E+01 CD 725 BOND = 41.7441 ANGLE = 180.9962 DIHED = 482.7240 VDWAALS = -875.0117 EEL = -8234.7437 EGB = -1507.6772 1-4 VDW = 335.4306 1-4 EEL = 5955.7170 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -3.6305E+03 1.2248E+00 1.2879E+01 HZ1 282 BOND = 43.4499 ANGLE = 183.2830 DIHED = 481.0710 VDWAALS = -878.2424 EEL = -8225.6916 EGB = -1511.6050 1-4 VDW = 330.8604 1-4 EEL = 5946.3757 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 250 -3.6368E+03 1.2415E+00 1.2856E+01 HZ1 282 BOND = 44.7024 ANGLE = 184.6987 DIHED = 479.5161 VDWAALS = -880.2588 EEL = -8219.4005 EGB = -1514.7529 1-4 VDW = 328.1447 1-4 EEL = 5940.5637 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 300 -3.6371E+03 1.2144E+00 1.2854E+01 HZ1 282 BOND = 44.7160 ANGLE = 184.7423 DIHED = 479.4359 VDWAALS = -880.3769 EEL = -8219.1843 EGB = -1514.7866 1-4 VDW = 328.0266 1-4 EEL = 5940.2965 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 350 -3.6374E+03 1.2014E+00 1.2853E+01 HZ1 282 BOND = 44.7385 ANGLE = 184.7862 DIHED = 479.3761 VDWAALS = -880.4377 EEL = -8218.9691 EGB = -1514.9080 1-4 VDW = 327.9426 1-4 EEL = 5940.1134 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 400 -3.6376E+03 1.2020E+00 1.2851E+01 HZ1 282 BOND = 44.7808 ANGLE = 184.8341 DIHED = 479.3109 VDWAALS = -880.5066 EEL = -8218.7441 EGB = -1515.0265 1-4 VDW = 327.8518 1-4 EEL = 5939.9143 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 450 -3.6378E+03 1.1994E+00 1.2850E+01 HZ1 282 BOND = 44.8170 ANGLE = 184.8797 DIHED = 479.2479 VDWAALS = -880.5715 EEL = -8218.5265 EGB = -1515.1440 1-4 VDW = 327.7654 1-4 EEL = 5939.7246 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 500 -3.6380E+03 1.2039E+00 1.2849E+01 HZ1 282 BOND = 44.8600 ANGLE = 184.9229 DIHED = 479.1876 VDWAALS = -880.6346 EEL = -8218.3246 EGB = -1515.2484 1-4 VDW = 327.6837 1-4 EEL = 5939.5445 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 500 -3.6380E+03 1.2039E+00 1.2849E+01 HZ1 282 BOND = 44.8600 ANGLE = 184.9229 DIHED = 479.1876 VDWAALS = -880.6346 EEL = -8218.3246 EGB = -1515.2484 1-4 VDW = 327.6837 1-4 EEL = 5939.5445 RESTRAINT = 0.0000 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 40.97 (21.19% of Gen B) | Calc gb diag 74.48 (38.53% of Gen B) | Calc gb off-diag 77.86 (40.27% of Gen B) | Gen Born time 193.32 (100.0% of Nonbo) | Nonbond force 193.32 (99.33% of Force) | Bond/Angle/Dihedral 1.30 ( 0.67% of Force) | Force time 194.62 (100.0% of Runmd) | Runmd Time 194.62 (100.0% of Total) | Other 0.13 ( 0.06% of Total) | Total time 194.75 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 15:59:26.254 on 06/18/2006 | Setup done at 15:59:26.298 on 06/18/2006 | Run done at 16:02:41.008 on 06/18/2006 | wallclock() was called 9008 times