------------------------------------------------------- Amber 7 SANDER Scripps/UCSF 2002 ------------------------------------------------------- | Thu Jul 11 17:46:33 2002 [-O]verwriting output File Assignments: | MDIN: min.in | MDOUT: 2qwe.min.out |INPCRD: 2qwe.rst | PARM: 2qwe.tpp |RESTRT: 2qwe.min.xyz | REFC: 2qwe.rst | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: #200 steps of minimization, distance-dependent dielectric in AMBER7 &cntrl maxcyc=200, imin=1, ntmin=1, ncyc=100, nsnb=20, igb=0,ntb=0,cut=10.0, dielc=1.0, ntpr=10, ntr=1, &end &ewald eedmeth=5, &end restrain protein atoms except H, ligand, and wat 32.0 FIND * CT * * * C * * * C* * * SEARCH RES 1 388 END restrain protein atoms except H 32.0 FIND * CA * * * CB * * * CC * * * CK * * * CM * * * CN * * * CQ * * * CR * * * CV * * * CW * * SEARCH RES 1 388 END restrain protein atoms except H 32.0 FIND * N3 * * * N * * * N* * * * N2 * * * NA * * * NB * * * NC * * SEARCH RES 1 388 END restrain protein atoms except H 32.0 FIND * OH * * * OS * * * O * * * O2 * * * P * * * S * * * SH * * SEARCH RES 1 388 END END -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: SGIFFT MEM_ALLOC MPI RLE ROWAT HAS_FTN_ERFC | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation | New format PARM file being parsed. | Version = 1.000 Date = 05/28/02 Time = 13:10:47 NATOM = 7150 NTYPES = 18 NBONH = 4055 MBONA = 3186 NTHETH = 6617 MTHETA = 4349 NPHIH = 12102 MPHIA = 7752 NHPARM = 0 NPARM = 0 NNB = 34744 NRES = 770 NBONA = 3186 NTHETA = 4349 NPHIA = 7752 NUMBND = 65 NUMANG = 135 NPTRA = 51 NATYP = 44 NPHB = 1 IFBOX = 0 NMXRS = 43 IFCAP = 0 NEXTRA = 0 | Memory Use Allocated | Real 598871 | Hollerith 43672 | Integer 1833041 | Max Pairs 3530057 | Max Rstack 2000000 | 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 = 10, 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 = 20 ipol = 0, gbsa = 0 dielc = 1.00000, cut = 10.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 1 Energy minimization: maxcyc = 200, ncyc = 100, ntmin = 1 dx0 = 0.01000, dxm = 0.50000, drms = 0.00010 | PLEVEL = 1: runmd parallelization, no EKCMR LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES ----- READING GROUP 1; TITLE: restrain protein atoms except H, ligand, and wat GROUP 1 HAS HARMONIC CONSTRAINTS 32.00000 ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE INCLUDED IN GROUP BELOW GRAPH NAME = * SYMBOL = CT TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = C TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = C* TREE SYMBOL = * RESIDUE TYPE = * GRP 1 RES 1 TO 388 Number of atoms in this group = 1628 ----- READING GROUP 2; TITLE: restrain protein atoms except H GROUP 2 HAS HARMONIC CONSTRAINTS 32.00000 ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE INCLUDED IN GROUP BELOW GRAPH NAME = * SYMBOL = CA TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = CB TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = CC TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = CK TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = CM TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = CN TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = CQ TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = CR TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = CV TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = CW TREE SYMBOL = * RESIDUE TYPE = * GRP 2 RES 1 TO 388 Number of atoms in this group = 286 ----- READING GROUP 3; TITLE: restrain protein atoms except H GROUP 3 HAS HARMONIC CONSTRAINTS 32.00000 ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE INCLUDED IN GROUP BELOW GRAPH NAME = * SYMBOL = N3 TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = N TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = N* TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = N2 TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = NA TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = NB TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = NC TREE SYMBOL = * RESIDUE TYPE = * GRP 3 RES 1 TO 388 Number of atoms in this group = 536 ----- READING GROUP 4; TITLE: restrain protein atoms except H GROUP 4 HAS HARMONIC CONSTRAINTS 32.00000 ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE INCLUDED IN GROUP BELOW GRAPH NAME = * SYMBOL = OH TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = OS TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = O TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = O2 TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = P TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = S TREE SYMBOL = * RESIDUE TYPE = * GRAPH NAME = * SYMBOL = SH TREE SYMBOL = * RESIDUE TYPE = * GRP 4 RES 1 TO 388 Number of atoms in this group = 615 ----- END OF GROUP READ ----- -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps | Reorder water Setup: | ----- Reordering water will NOT be done | Does not work with minimization | Number of triangulated 3-point waters found: 380 | Atom division among processors: | 0 7150 | Running AMBER/MPI version on 1 nodes Sum of charges from parm topology file = 0.99999986 Assuming uniform neutralizing plasma -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- eedmeth=5: Using 1/r dielectric --------------------------------------------------- | Local SIZE OF NONBOND LIST = 1988506 | TOTAL SIZE OF NONBOND LIST = 1988506 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -9.9648E+02 4.2334E+01 1.7804E+03 HD2 2370 BOND = 5856.8525 ANGLE = 1255.5943 DIHED = 1922.2507 VDWAALS = -2327.5121 EEL = -14188.0375 HBOND = 0.0000 1-4 VDW = 1769.9285 1-4 EEL = 4714.4460 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 10 -2.3702E+03 3.4260E+01 6.0555E+02 HD2 2370 BOND = 4612.2427 ANGLE = 1226.6158 DIHED = 1920.4721 VDWAALS = -2445.9781 EEL = -14160.7239 HBOND = 0.0000 1-4 VDW = 1764.3673 1-4 EEL = 4712.7194 RESTRAINT = 0.1043 EAMBER = -2370.2847 NSTEP ENERGY RMS GMAX NAME NUMBER 20 -6.8671E+03 8.0422E+00 6.2753E+01 O 6032 BOND = 597.6969 ANGLE = 995.0782 DIHED = 1905.3904 VDWAALS = -2661.6422 EEL = -14121.6747 HBOND = 0.0000 1-4 VDW = 1712.4418 1-4 EEL = 4695.6864 RESTRAINT = 9.8772 EAMBER = -6877.0232 NSTEP ENERGY RMS GMAX NAME NUMBER 30 -8.9311E+03 3.8481E+00 3.2556E+01 H2 7117 BOND = 375.3349 ANGLE = 649.3361 DIHED = 1910.4912 VDWAALS = -2959.1946 EEL = -15198.0775 HBOND = 0.0000 1-4 VDW = 1542.7306 1-4 EEL = 4622.7817 RESTRAINT = 125.4978 EAMBER = -9056.5977 NSTEP ENERGY RMS GMAX NAME NUMBER 40 -9.2943E+03 4.4053E+00 3.6226E+01 H1 6684 BOND = 422.8658 ANGLE = 637.6192 DIHED = 1914.9271 VDWAALS = -2974.8010 EEL = -15561.4434 HBOND = 0.0000 1-4 VDW = 1507.1665 1-4 EEL = 4593.9777 RESTRAINT = 165.3933 EAMBER = -9459.6882 NSTEP ENERGY RMS GMAX NAME NUMBER 50 -9.5733E+03 1.2366E+00 1.4623E+01 HO8 6004 BOND = 318.9299 ANGLE = 637.1869 DIHED = 1918.6011 VDWAALS = -2965.8499 EEL = -15735.7023 HBOND = 0.0000 1-4 VDW = 1486.2854 1-4 EEL = 4574.5239 RESTRAINT = 192.7327 EAMBER = -9766.0250 NSTEP ENERGY RMS GMAX NAME NUMBER 60 -9.7233E+03 1.0884E+00 1.6077E+01 HO8 6004 BOND = 335.3642 ANGLE = 638.4599 DIHED = 1921.8400 VDWAALS = -2942.5834 EEL = -15922.6032 HBOND = 0.0000 1-4 VDW = 1472.9491 1-4 EEL = 4560.2651 RESTRAINT = 212.9796 EAMBER = -9936.3083 NSTEP ENERGY RMS GMAX NAME NUMBER 70 -9.8912E+03 1.3714E+00 1.5903E+01 HO8 6004 BOND = 341.9018 ANGLE = 640.1490 DIHED = 1924.7587 VDWAALS = -2910.7984 EEL = -16129.1874 HBOND = 0.0000 1-4 VDW = 1463.5458 1-4 EEL = 4549.4958 RESTRAINT = 228.9768 EAMBER = -10120.1347 NSTEP ENERGY RMS GMAX NAME NUMBER 80 -9.9890E+03 2.4498E+00 2.5590E+01 H2 6580 BOND = 344.7488 ANGLE = 641.6039 DIHED = 1927.1012 VDWAALS = -2875.8563 EEL = -16266.5878 HBOND = 0.0000 1-4 VDW = 1457.5216 1-4 EEL = 4542.0668 RESTRAINT = 240.4025 EAMBER = -10229.4018 NSTEP ENERGY RMS GMAX NAME NUMBER 90 -1.0073E+04 2.6074E+00 3.0501E+01 H2 6580 BOND = 356.1905 ANGLE = 642.6144 DIHED = 1929.1735 VDWAALS = -2837.2259 EEL = -16402.8449 HBOND = 0.0000 1-4 VDW = 1453.1777 1-4 EEL = 4536.5251 RESTRAINT = 249.1099 EAMBER = -10322.3896 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -1.0216E+04 8.7114E-01 1.0975E+01 H1 6168 BOND = 411.3602 ANGLE = 642.7493 DIHED = 1931.0422 VDWAALS = -2796.4106 EEL = -16642.3178 HBOND = 0.0000 1-4 VDW = 1449.6567 1-4 EEL = 4532.7554 RESTRAINT = 255.6284 EAMBER = -10471.1646 NSTEP ENERGY RMS GMAX NAME NUMBER 110 -1.0228E+04 1.0555E+00 1.1382E+01 H2 6580 BOND = 389.9274 ANGLE = 642.8861 DIHED = 1931.1979 VDWAALS = -2791.3463 EEL = -16639.1546 HBOND = 0.0000 1-4 VDW = 1449.5571 1-4 EEL = 4532.1963 RESTRAINT = 256.3473 EAMBER = -10484.7361 NSTEP ENERGY RMS GMAX NAME NUMBER 120 -1.0228E+04 1.0538E+00 1.1343E+01 H2 6580 BOND = 389.9728 ANGLE = 642.8858 DIHED = 1931.1982 VDWAALS = -2791.3411 EEL = -16639.2292 HBOND = 0.0000 1-4 VDW = 1449.5563 1-4 EEL = 4532.1962 RESTRAINT = 256.3480 EAMBER = -10484.7610 NSTEP ENERGY RMS GMAX NAME NUMBER 130 -1.0226E+04 1.0439E+00 1.1119E+01 H2 6580 BOND = 390.2392 ANGLE = 642.8842 DIHED = 1931.2002 VDWAALS = -2791.3077 EEL = -16637.0435 HBOND = 0.0000 1-4 VDW = 1449.5514 1-4 EEL = 4532.1951 RESTRAINT = 256.3521 EAMBER = -10482.2811 NSTEP ENERGY RMS GMAX NAME NUMBER 140 -1.0227E+04 1.0442E+00 1.1125E+01 H2 6580 BOND = 390.2318 ANGLE = 642.8843 DIHED = 1931.2001 VDWAALS = -2791.3081 EEL = -16638.1021 HBOND = 0.0000 1-4 VDW = 1449.5515 1-4 EEL = 4532.1951 RESTRAINT = 256.3519 EAMBER = -10483.3473 NSTEP ENERGY RMS GMAX NAME NUMBER 150 -1.0226E+04 1.0120E+00 1.0374E+01 H2 6580 BOND = 391.1365 ANGLE = 642.8792 DIHED = 1931.2067 VDWAALS = -2791.1931 EEL = -16637.8945 HBOND = 0.0000 1-4 VDW = 1449.5349 1-4 EEL = 4532.1913 RESTRAINT = 256.3659 EAMBER = -10482.1389 NSTEP ENERGY RMS GMAX NAME NUMBER 160 -1.0226E+04 1.0132E+00 1.0402E+01 H2 6580 BOND = 391.1022 ANGLE = 642.8794 DIHED = 1931.2065 VDWAALS = -2791.1974 EEL = -16638.3825 HBOND = 0.0000 1-4 VDW = 1449.5355 1-4 EEL = 4532.1915 RESTRAINT = 256.3654 EAMBER = -10482.6649 NSTEP ENERGY RMS GMAX NAME NUMBER 170 -1.0226E+04 8.7606E-01 1.0774E+01 H1 6168 BOND = 414.7762 ANGLE = 642.8176 DIHED = 1931.3576 VDWAALS = -2788.4889 EEL = -16664.3746 HBOND = 0.0000 1-4 VDW = 1449.1629 1-4 EEL = 4532.0944 RESTRAINT = 256.7004 EAMBER = -10482.6546 NSTEP ENERGY RMS GMAX NAME NUMBER 180 -1.0230E+04 8.3936E-01 1.0612E+01 H1 6168 BOND = 412.5981 ANGLE = 642.8193 DIHED = 1931.3455 VDWAALS = -2788.7107 EEL = -16666.2717 HBOND = 0.0000 1-4 VDW = 1449.1927 1-4 EEL = 4532.1022 RESTRAINT = 256.6731 EAMBER = -10486.9246 NSTEP ENERGY RMS GMAX NAME NUMBER 190 -1.0271E+04 1.7105E+00 2.2926E+01 H2 6580 BOND = 381.7690 ANGLE = 643.1504 DIHED = 1931.6407 VDWAALS = -2779.0168 EEL = -16686.3680 HBOND = 0.0000 1-4 VDW = 1448.9628 1-4 EEL = 4531.1135 RESTRAINT = 257.9880 EAMBER = -10528.7485 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -1.0296E+04 1.0072E+00 1.0772E+01 H1 6168 BOND = 425.1211 ANGLE = 642.9032 DIHED = 1931.8097 VDWAALS = -2776.8969 EEL = -16756.8387 HBOND = 0.0000 1-4 VDW = 1448.4498 1-4 EEL = 4531.2018 RESTRAINT = 258.1816 EAMBER = -10554.2501 MAXIMUM NUMBER OF F EVALUATION EXCEEDED FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 200 -1.0296E+04 1.0072E+00 1.0772E+01 H1 6168 BOND = 425.1211 ANGLE = 642.9032 DIHED = 1931.8097 VDWAALS = -2776.8969 EEL = -16756.8387 HBOND = 0.0000 1-4 VDW = 1448.4498 1-4 EEL = 4531.2018 RESTRAINT = 258.1816 EAMBER = -10554.2501 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.06 ( 0.02% of Total) | Ewald setup time 0.06 ( 0.03% of List ) | Check list validity 0.17 ( 0.10% of List ) | Map frac coords 0.31 ( 0.18% of List ) | Grid unit cell 19.48 (11.17% of List ) | Grid image cell 1.05 ( 0.60% of List ) | Build the list 153.23 (87.90% of List ) | Other 0.02 ( 0.01% of List ) | List time 174.32 (65.96% of Nonbo) | Direct Ewald time 87.48 (97.24% of Ewald) | Finish NB virial 0.24 ( 0.26% of Ewald) | Other 2.25 ( 2.50% of Ewald) | Ewald time 89.97 (34.04% of Nonbo) | Nonbond force 264.29 (95.21% of Force) | Bond energy 0.61 ( 0.22% of Force) | Angle energy 2.36 ( 0.85% of Force) | Dihedral energy 9.88 ( 3.56% of Force) | Other 0.46 ( 0.16% of Force) | Force time 277.59 (100.0% of Runmd) | Runmd Time 277.59 (97.86% of Total) | Other 6.02 ( 2.12% of Total) | Total time 283.67 (100.0% of ALL ) | Highest rstack allocated: 2700 | Highest istack allocated: 1242362 | Setup wallclock 4 seconds | Nonsetup wallclock 280 seconds