------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | Run on 06/25/2009 at 19:05:08 [-O]verwriting output File Assignments: | MDIN: min1.in | MDOUT: ./FK506_min.out |INPCRD: ./FK506.crd | PARM: ./FK506.top |RESTRT: ./FK506_min.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: ./moke1 |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj | Here is the input file: moke &cntrl imin=1, maxcyc=2000, cut=10.0, ntpr=100, ntb=0, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation |Largest sphere to fit in unit cell has radius = 34.676 | New format PARM file being parsed. | Version = 1.000 Date = 06/25/09 Time = 19:03:52 NATOM = 126 NTYPES = 10 NBONH = 69 MBONA = 60 NTHETH = 159 MTHETA = 86 NPHIH = 272 MPHIA = 180 NHPARM = 0 NPARM = 0 NNB = 730 NRES = 1 NBONA = 60 NTHETA = 86 NPHIA = 180 NUMBND = 15 NUMANG = 41 NPTRA = 32 NATYP = 11 NPHB = 0 IFBOX = 0 NMXRS = 126 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 9047 | Hollerith 759 | Integer 32091 | Max Pairs 7875 | nblistReal 1512 | nblist Int 926378 | Total 3860 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- FK5 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 = 100, 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 = 10.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 2000, ncyc = 10, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- FK5 begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 Sum of charges from parm topology file = 0.00020000 Forcing neutrality... -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- eedmeth=4: Setting switch to one everywhere --------------------------------------------------- | Local SIZE OF NONBOND LIST = 5790 | TOTAL SIZE OF NONBOND LIST = 5790 NSTEP ENERGY RMS GMAX NAME NUMBER 1 2.0724E+02 1.2934E+01 8.9581E+01 C8 19 BOND = 14.0653 ANGLE = 28.2388 DIHED = 68.4164 VDWAALS = -10.4061 EEL = -2.6744 HBOND = 0.0000 1-4 VDW = 35.7155 1-4 EEL = 73.8831 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 100 1.3581E+02 6.6866E-01 2.6213E+00 O4 22 BOND = 5.3052 ANGLE = 18.7105 DIHED = 65.8230 VDWAALS = -25.5328 EEL = -26.7988 HBOND = 0.0000 1-4 VDW = 24.9985 1-4 EEL = 73.3002 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 200 1.1753E+02 3.5089E-01 1.8148E+00 C8 19 BOND = 5.0874 ANGLE = 17.3477 DIHED = 64.3679 VDWAALS = -25.1017 EEL = -44.8459 HBOND = 0.0000 1-4 VDW = 25.3236 1-4 EEL = 75.3474 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 300 1.1669E+02 3.2050E-01 1.1930E+00 O12 118 BOND = 5.0840 ANGLE = 16.7625 DIHED = 63.3317 VDWAALS = -24.7942 EEL = -43.8075 HBOND = 0.0000 1-4 VDW = 25.1563 1-4 EEL = 74.9607 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 400 1.2044E+02 3.7021E-01 1.7662E+00 C30 107 BOND = 5.0658 ANGLE = 16.5799 DIHED = 62.8332 VDWAALS = -24.5460 EEL = -39.2929 HBOND = 0.0000 1-4 VDW = 25.1793 1-4 EEL = 74.6158 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 500 1.1654E+02 6.0733E-01 4.6424E+00 C22 81 BOND = 5.0517 ANGLE = 16.7228 DIHED = 62.3613 VDWAALS = -24.4292 EEL = -43.0021 HBOND = 0.0000 1-4 VDW = 25.0905 1-4 EEL = 74.7446 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 600 1.2237E+02 2.1363E-01 1.1206E+00 C22 81 BOND = 5.0340 ANGLE = 16.3939 DIHED = 62.2614 VDWAALS = -24.2946 EEL = -36.7516 HBOND = 0.0000 1-4 VDW = 25.1835 1-4 EEL = 74.5462 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 700 1.2315E+02 8.6958E-02 3.2880E-01 H68 88 BOND = 5.0609 ANGLE = 16.3805 DIHED = 62.2535 VDWAALS = -24.3123 EEL = -35.8187 HBOND = 0.0000 1-4 VDW = 25.1497 1-4 EEL = 74.4328 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 800 1.2310E+02 8.7649E-02 3.8702E-01 H68 88 BOND = 5.0576 ANGLE = 16.3427 DIHED = 62.2907 VDWAALS = -24.3193 EEL = -35.8034 HBOND = 0.0000 1-4 VDW = 25.1612 1-4 EEL = 74.3745 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 900 1.2050E+02 9.7356E-02 4.8586E-01 H68 88 BOND = 5.0352 ANGLE = 16.2998 DIHED = 62.3520 VDWAALS = -24.3590 EEL = -38.3233 HBOND = 0.0000 1-4 VDW = 25.1893 1-4 EEL = 74.3101 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1000 1.2130E+02 9.4752E-02 6.2184E-01 C9 21 BOND = 5.0218 ANGLE = 16.2607 DIHED = 62.4394 VDWAALS = -24.4261 EEL = -37.4070 HBOND = 0.0000 1-4 VDW = 25.2018 1-4 EEL = 74.2109 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1100 1.2072E+02 7.5349E-02 4.8512E-01 C22 81 BOND = 5.0097 ANGLE = 16.1969 DIHED = 62.5703 VDWAALS = -24.5145 EEL = -37.9057 HBOND = 0.0000 1-4 VDW = 25.2070 1-4 EEL = 74.1606 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1200 1.1954E+02 1.2229E-01 7.8827E-01 C24 86 BOND = 4.9843 ANGLE = 16.1186 DIHED = 62.7165 VDWAALS = -24.5926 EEL = -39.0641 HBOND = 0.0000 1-4 VDW = 25.2351 1-4 EEL = 74.1390 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1300 1.2530E+02 8.8756E-02 6.0495E-01 H69 119 BOND = 4.9579 ANGLE = 16.0257 DIHED = 62.8657 VDWAALS = -24.6665 EEL = -33.2072 HBOND = 0.0000 1-4 VDW = 25.2613 1-4 EEL = 74.0626 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1400 1.2633E+02 9.0420E-02 8.1592E-01 H69 119 BOND = 4.9276 ANGLE = 15.9739 DIHED = 62.9712 VDWAALS = -24.7289 EEL = -32.1498 HBOND = 0.0000 1-4 VDW = 25.2789 1-4 EEL = 74.0589 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1500 1.2721E+02 1.0860E-01 6.5953E-01 H69 119 BOND = 4.9048 ANGLE = 15.9035 DIHED = 63.0555 VDWAALS = -24.7757 EEL = -31.2101 HBOND = 0.0000 1-4 VDW = 25.2982 1-4 EEL = 74.0312 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1600 1.2665E+02 9.9092E-02 8.0616E-01 C22 81 BOND = 4.9294 ANGLE = 15.8740 DIHED = 63.1400 VDWAALS = -24.8640 EEL = -31.6992 HBOND = 0.0000 1-4 VDW = 25.2935 1-4 EEL = 73.9773 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1700 1.2687E+02 8.7035E-02 6.4995E-01 H69 119 BOND = 4.9320 ANGLE = 15.8686 DIHED = 63.2051 VDWAALS = -24.9386 EEL = -31.4073 HBOND = 0.0000 1-4 VDW = 25.2803 1-4 EEL = 73.9298 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1800 1.2577E+02 1.5936E-01 1.0819E+00 C8 19 BOND = 4.9156 ANGLE = 15.8122 DIHED = 63.2696 VDWAALS = -24.9794 EEL = -32.3627 HBOND = 0.0000 1-4 VDW = 25.3100 1-4 EEL = 73.8075 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1900 1.2572E+02 1.2715E-01 8.6769E-01 O10 87 BOND = 4.9967 ANGLE = 15.8915 DIHED = 63.2853 VDWAALS = -25.0846 EEL = -32.2662 HBOND = 0.0000 1-4 VDW = 25.1412 1-4 EEL = 73.7570 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 2000 1.2959E+02 7.7868E-02 6.7289E-01 C22 81 BOND = 4.9300 ANGLE = 15.7740 DIHED = 63.3036 VDWAALS = -25.0554 EEL = -28.3915 HBOND = 0.0000 1-4 VDW = 25.2805 1-4 EEL = 73.7456 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 2000 1.2959E+02 7.7868E-02 6.7289E-01 C22 81 BOND = 4.9300 ANGLE = 15.7740 DIHED = 63.3036 VDWAALS = -25.0554 EEL = -28.3915 HBOND = 0.0000 1-4 VDW = 25.2805 1-4 EEL = 73.7456 RESTRAINT = 0.0000 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.00 ( 0.04% of Total) | Build the list 0.33 (99.40% of List ) | Other 0.00 ( 0.60% of List ) | List time 0.33 (31.09% of Nonbo) | Short_ene time 0.67 (98.70% of Direc) | Other 0.01 ( 1.30% of Direc) | Direct Ewald time 0.68 (93.16% of Ewald) | Force Adjust 0.00 ( 0.41% of Ewald) | Virial junk 0.00 ( 0.25% of Ewald) | Start sycnronization 0.00 ( 0.26% of Ewald) | Other 0.04 ( 5.92% of Ewald) | Ewald time 0.72 (67.98% of Nonbo) | IPS excludes 0.00 ( 0.16% of Nonbo) | Other 0.01 ( 0.77% of Nonbo) | Nonbond force 1.07 (70.44% of Force) | Bond/Angle/Dihedral 0.44 (29.03% of Force) | Other 0.01 ( 0.52% of Force) | Force time 1.51 (100.0% of Runmd) | Runmd Time 1.51 (98.23% of Total) | Other 0.03 ( 1.73% of Total) | Total time 1.54 (100.0% of ALL ) | Highest rstack allocated: 570 | Highest istack allocated: 114 | Job began at 19:05:08.923 on 06/25/2009 | Setup done at 19:05:08.934 on 06/25/2009 | Run done at 19:05:10.464 on 06/25/2009 | wallclock() was called 46170 times