------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 03/30/2007 at 15:32:17 [-O]verwriting output File Assignments: | MDIN: anneal.in | MDOUT: try.ann.out |INPCRD: try4.min.x | PARM: delprmtop |RESTRT: try.ann.x | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: try.ann.traj |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: simulated annealing protocol, 20 ps &cntrl nstlim=100, pencut=-0.001, nmropt=1, ntpr=5, ntt=1, ntwx=5, cut=18.0, ntb=0, vlimit=10, / &ewald eedmeth=5, / LISTOUT=POUT DISANG=RST.bb / # #Simple simulated annealing algorithm: # #from steps 0 to 30: heat the system to 600K #from steps 31-70: re-cool to low temperatures with long tautp #from steps 71-100: final cooling with short tautp # &wt type='TEMP0', istep1=0,istep2=30,value1=0, value2=600., / &wt type='TEMP0', istep1=31, istep2=70, value1=600.0, value2=100.0, / &wt type='TEMP0', istep1=71, istep2=100, value1=0.0, value2=0.0, / &wt type='TAUTP', istep1=0,istep2=20,value1=0.4, value2=0.4, / &wt type='TAUTP', istep1=21,istep2=45,value1=4.0 value2=4.0, / &wt type='TAUTP', istep1=46,istep2=70,value1=1.0, value2=1.0, / &wt type='TAUTP', istep1=71,istep2=100,value1=0.1, value2=0.05, / &wt type='REST', istep1=0,istep2=50,value1=0.1, value2=1.0, / &wt type='REST', istep1=51,istep2=100,value1=1.0, value2=1.0, / &wt type='END' / group input for restrained atoms restraint_wt=1.0 restraintmask="@23-40" LISTOUT=POUT DISANG=RST.bb / -------------------------------------------------------------------------------- 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 = 33.604 | New format PARM file being parsed. | Version = 1.000 Date = 03/29/07 Time = 12:30:39 NATOM = 40 NTYPES = 8 NBONH = 18 MBONA = 23 NTHETH = 39 MTHETA = 29 NPHIH = 80 MPHIA = 45 NHPARM = 0 NPARM = 0 NNB = 206 NRES = 2 NBONA = 23 NTHETA = 29 NPHIA = 45 NUMBND = 11 NUMANG = 19 NPTRA = 21 NATYP = 9 NPHB = 0 IFBOX = 0 NMXRS = 20 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 3249 | Hollerith 244 | Integer 23546 | Max Pairs 780 | nblistReal 480 | nblist Int 96689 | Total 502 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- PHE General flags: imin = 0, nmropt = 1 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 5, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 5, 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 = 18.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 100, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00100, vlimit = 10.00000 Berendsen (weak-coupling) temperature regulation: temp0 = 300.00000, tempi = 0.00000, tautp = 1.00000 NMR refinement options: iscale = 0, noeskp = 1, ipnlty = 1, mxsub = 1 scalm = 100.00000, pencut = -0.00100, tausw = 0.10000 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- PHE begin time read from input coords = 0.000 ps Begin reading energy term weight changes/NMR restraints WEIGHT CHANGES: TEMP0 0 30 0.000000 600.000000 0 0 TEMP0 31 70 600.000000 100.000000 0 0 TEMP0 71 100 0.000000 0.000000 0 0 TAUTP 0 20 0.400000 0.400000 0 0 TAUTP 21 45 4.000000 4.000000 0 0 TAUTP 46 70 1.000000 1.000000 0 0 TAUTP 71 100 0.100000 0.050000 0 0 REST 0 50 0.100000 1.000000 0 0 REST 51 100 1.000000 1.000000 0 0 RESTRAINTS: No valid redirection requests found ** No restraint defined ** Done reading weight changes/NMR restraints Number of triangulated 3-point waters found: 0 Sum of charges from parm topology file = -0.00000000 Forcing neutrality... -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- eedmeth=5: Using 1/r dielectric --------------------------------------------------- | Local SIZE OF NONBOND LIST = 577 | TOTAL SIZE OF NONBOND LIST = 577 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = 32.3685 EKtot = 0.0000 EPtot = 32.3685 BOND = 1.1296 ANGLE = 3.2727 DIHED = 8.1547 1-4 NB = 10.6702 1-4 EEL = 49.7401 VDWAALS = -3.6139 EELEC = -36.9849 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 5 TIME(PS) = 0.005 TEMP(K) = 1.53 PRESS = 0.0 Etot = 32.3722 EKtot = 0.1733 EPtot = 32.1988 BOND = 1.0977 ANGLE = 3.2033 DIHED = 8.1086 1-4 NB = 10.6615 1-4 EEL = 49.7110 VDWAALS = -3.6005 EELEC = -36.9827 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 10 TIME(PS) = 0.010 TEMP(K) = 3.91 PRESS = 0.0 Etot = 32.4466 EKtot = 0.4424 EPtot = 32.0042 BOND = 1.1610 ANGLE = 3.1152 DIHED = 8.0284 1-4 NB = 10.6477 1-4 EEL = 49.6189 VDWAALS = -3.5776 EELEC = -36.9894 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 15 TIME(PS) = 0.015 TEMP(K) = 5.54 PRESS = 0.0 Etot = 32.6334 EKtot = 0.6271 EPtot = 32.0063 BOND = 1.2155 ANGLE = 3.0738 DIHED = 8.0996 1-4 NB = 10.6407 1-4 EEL = 49.5184 VDWAALS = -3.5401 EELEC = -37.0016 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 20 TIME(PS) = 0.020 TEMP(K) = 8.04 PRESS = 0.0 Etot = 32.9724 EKtot = 0.9111 EPtot = 32.0613 BOND = 1.2358 ANGLE = 3.0279 DIHED = 8.2544 1-4 NB = 10.6544 1-4 EEL = 49.4601 VDWAALS = -3.5321 EELEC = -37.0393 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 25 TIME(PS) = 0.025 TEMP(K) = 9.79 PRESS = 0.0 Etot = 33.2040 EKtot = 1.1093 EPtot = 32.0947 BOND = 1.2462 ANGLE = 2.9845 DIHED = 8.3366 1-4 NB = 10.7235 1-4 EEL = 49.4572 VDWAALS = -3.5629 EELEC = -37.0904 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 30 TIME(PS) = 0.030 TEMP(K) = 11.02 PRESS = 0.0 Etot = 33.2781 EKtot = 1.2484 EPtot = 32.0297 BOND = 1.2648 ANGLE = 2.9425 DIHED = 8.3041 1-4 NB = 10.8015 1-4 EEL = 49.4880 VDWAALS = -3.5888 EELEC = -37.1823 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 35 TIME(PS) = 0.035 TEMP(K) = 13.23 PRESS = 0.0 Etot = 33.3622 EKtot = 1.4985 EPtot = 31.8637 BOND = 1.2718 ANGLE = 2.8271 DIHED = 8.2347 1-4 NB = 10.8971 1-4 EEL = 49.5555 VDWAALS = -3.6387 EELEC = -37.2837 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 40 TIME(PS) = 0.040 TEMP(K) = 15.09 PRESS = 0.0 Etot = 33.4378 EKtot = 1.7089 EPtot = 31.7289 BOND = 1.1699 ANGLE = 2.7874 DIHED = 8.2448 1-4 NB = 10.9697 1-4 EEL = 49.6401 VDWAALS = -3.6944 EELEC = -37.3886 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 45 TIME(PS) = 0.045 TEMP(K) = 16.63 PRESS = 0.0 Etot = 33.5035 EKtot = 1.8832 EPtot = 31.6203 BOND = 1.0512 ANGLE = 2.7808 DIHED = 8.2753 1-4 NB = 11.0427 1-4 EEL = 49.6968 VDWAALS = -3.8218 EELEC = -37.4048 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 50 TIME(PS) = 0.050 TEMP(K) = 20.39 PRESS = 0.0 Etot = 33.6572 EKtot = 2.3092 EPtot = 31.3480 BOND = 0.8788 ANGLE = 2.8552 DIHED = 8.2184 1-4 NB = 11.0747 1-4 EEL = 49.6401 VDWAALS = -3.9694 EELEC = -37.3499 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 55 TIME(PS) = 0.055 TEMP(K) = 24.74 PRESS = 0.0 Etot = 33.8422 EKtot = 2.8021 EPtot = 31.0401 BOND = 0.8858 ANGLE = 2.9042 DIHED = 8.1210 1-4 NB = 11.0315 1-4 EEL = 49.4849 VDWAALS = -4.1384 EELEC = -37.2490 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 60 TIME(PS) = 0.060 TEMP(K) = 26.90 PRESS = 0.0 Etot = 33.9876 EKtot = 3.0472 EPtot = 30.9404 BOND = 1.0950 ANGLE = 2.9703 DIHED = 8.0944 1-4 NB = 10.9276 1-4 EEL = 49.3081 VDWAALS = -4.2530 EELEC = -37.2020 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 65 TIME(PS) = 0.065 TEMP(K) = 28.98 PRESS = 0.0 Etot = 34.0946 EKtot = 3.2820 EPtot = 30.8126 BOND = 1.3793 ANGLE = 2.8079 DIHED = 8.1384 1-4 NB = 10.7716 1-4 EEL = 49.2243 VDWAALS = -4.3116 EELEC = -37.1974 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 70 TIME(PS) = 0.070 TEMP(K) = 30.97 PRESS = 0.0 Etot = 34.1645 EKtot = 3.5079 EPtot = 30.6566 BOND = 1.5458 ANGLE = 2.5699 DIHED = 8.1895 1-4 NB = 10.6849 1-4 EEL = 49.2320 VDWAALS = -4.3312 EELEC = -37.2343 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 75 TIME(PS) = 0.075 TEMP(K) = 32.31 PRESS = 0.0 Etot = 34.0713 EKtot = 3.6603 EPtot = 30.4111 BOND = 1.5376 ANGLE = 2.3792 DIHED = 8.2057 1-4 NB = 10.6601 1-4 EEL = 49.2771 VDWAALS = -4.3782 EELEC = -37.2703 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 80 TIME(PS) = 0.080 TEMP(K) = 33.59 PRESS = 0.0 Etot = 33.8654 EKtot = 3.8050 EPtot = 30.0604 BOND = 1.3421 ANGLE = 2.2830 DIHED = 8.2307 1-4 NB = 10.7307 1-4 EEL = 49.2743 VDWAALS = -4.4845 EELEC = -37.3159 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 85 TIME(PS) = 0.085 TEMP(K) = 34.23 PRESS = 0.0 Etot = 33.6307 EKtot = 3.8777 EPtot = 29.7530 BOND = 1.1041 ANGLE = 2.2980 DIHED = 8.2773 1-4 NB = 10.7999 1-4 EEL = 49.1861 VDWAALS = -4.5948 EELEC = -37.3176 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 90 TIME(PS) = 0.090 TEMP(K) = 32.64 PRESS = 0.0 Etot = 33.3733 EKtot = 3.6975 EPtot = 29.6758 BOND = 1.0530 ANGLE = 2.3312 DIHED = 8.3146 1-4 NB = 10.8850 1-4 EEL = 49.0333 VDWAALS = -4.6804 EELEC = -37.2609 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 95 TIME(PS) = 0.095 TEMP(K) = 30.75 PRESS = 0.0 Etot = 33.1002 EKtot = 3.4834 EPtot = 29.6168 BOND = 0.9914 ANGLE = 2.3441 DIHED = 8.3280 1-4 NB = 10.9316 1-4 EEL = 48.9251 VDWAALS = -4.7353 EELEC = -37.1682 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 100 TIME(PS) = 0.100 TEMP(K) = 29.54 PRESS = 0.0 Etot = 32.7993 EKtot = 3.3465 EPtot = 29.4528 BOND = 1.0432 ANGLE = 2.2235 DIHED = 8.2621 1-4 NB = 10.9378 1-4 EEL = 48.9411 VDWAALS = -4.8098 EELEC = -37.1451 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== A V E R A G E S O V E R 100 S T E P S NSTEP = 100 TIME(PS) = 0.100 TEMP(K) = 19.91 PRESS = 0.0 Etot = 33.3836 EKtot = 2.2550 EPtot = 31.1286 BOND = 1.1805 ANGLE = 2.7571 DIHED = 8.2116 1-4 NB = 10.8183 1-4 EEL = 49.3993 VDWAALS = -4.0380 EELEC = -37.2004 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== R M S F L U C T U A T I O N S NSTEP = 100 TIME(PS) = 0.100 TEMP(K) = 11.24 PRESS = 0.0 Etot = 0.5428 EKtot = 1.2736 EPtot = 0.9247 BOND = 0.1803 ANGLE = 0.3087 DIHED = 0.0862 1-4 NB = 0.1434 1-4 EEL = 0.2336 VDWAALS = 0.4373 EELEC = 0.1298 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NMR restraints on final step: -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.00 ( 0.58% of Total) | Fast Water setup 0.00 ( 0.01% of Total) | Build the list 0.00 (90.69% of List ) | Other 0.00 ( 9.31% of List ) | List time 0.00 (14.93% of Nonbo) | Short_ene time 0.01 (96.02% of Direc) | Other 0.00 ( 3.98% of Direc) | Direct Ewald time 0.02 (82.60% of Ewald) | Force Adjust 0.00 (11.82% of Ewald) | Virial junk 0.00 ( 1.05% of Ewald) | Start sycnronization 0.00 ( 1.38% of Ewald) | Other 0.00 ( 3.14% of Ewald) | Ewald time 0.02 (81.37% of Nonbo) | IPS excludes 0.00 ( 0.64% of Nonbo) | Other 0.00 ( 3.06% of Nonbo) | Nonbond force 0.02 (18.89% of Force) | Bond/Angle/Dihedral 0.10 (79.75% of Force) | Other 0.00 ( 1.36% of Force) | Force time 0.12 (77.95% of Runmd) | Verlet update time 0.03 (20.91% of Runmd) | Other 0.00 ( 1.14% of Runmd) | Runmd Time 0.15 (90.20% of Total) | Other 0.02 ( 9.21% of Total) | Total time 0.17 (99.84% of ALL ) | Highest rstack allocated: 145 | Highest istack allocated: 29 | Job began at 15:32:17.081 on 03/30/2007 | Setup done at 15:32:17.098 on 03/30/2007 | Run done at 15:32:17.251 on 03/30/2007 | wallclock() was called 2735 times