------------------------------------------------------- Amber 7 SANDER Scripps/UCSF 2002 ------------------------------------------------------- | Tue Nov 30 22:16:27 2004 [-O]verwriting output File Assignments: | MDIN: p2Im.in | MDOUT: 1bdc.nnNb.out |INPCRD: 1bdc.nnN.crd | PARM: 1bdc.nnN.top |RESTRT: 1bdc.nnNminb.crd | REFC: 1bdc.nnN.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=1,dielc=4,cut=300.0, maxcyc=1000, ncyc=500, &end &ewald eedmeth=5, &end restraint 1 25.0 RES 10 19 RES 25 37 RES 42 55 END 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 = 11/28/04 Time = 12:55:55 NATOM = 941 NTYPES = 13 NBONH = 463 MBONA = 485 NTHETH = 1062 MTHETA = 654 NPHIH = 2032 MPHIA = 1226 NHPARM = 0 NPARM = 0 NNB = 5196 NRES = 60 NBONA = 485 NTHETA = 654 NPHIA = 1226 NUMBND = 31 NUMANG = 64 NPTRA = 32 NATYP = 22 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 | Memory Use Allocated | Real 77617 | Hollerith 5708 | Integer 1292129 | Max Pairs 442270 | 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 = 1 Energy minimization: maxcyc = 1000, ncyc = 500, ntmin = 1 dx0 = 0.01000, dxm = 0.50000, drms = 0.00010 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES ----- READING GROUP 1; TITLE: restraint 1 GROUP 1 HAS HARMONIC CONSTRAINTS 25.00000 GRP 1 RES 10 TO 19 GRP 1 RES 25 TO 37 GRP 1 RES 42 TO 55 Number of atoms in this group = 588 ----- END OF GROUP READ ----- -------------------------------------------------------------------------------- 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 = -1.00000001 Assuming uniform neutralizing plasma -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- eedmeth=5: Using 1/r dielectric --------------------------------------------------- | Local SIZE OF NONBOND LIST = 437123 | TOTAL SIZE OF NONBOND LIST = 437123 NSTEP ENERGY RMS GMAX NAME NUMBER 1 4.2081E+02 1.9983E+00 2.1735E+01 NE 455 BOND = 25.1839 ANGLE = 122.4492 DIHED = 608.2743 VDWAALS = -408.4175 EEL = -338.1201 HBOND = 0.0000 1-4 VDW = 204.7847 1-4 EEL = 206.6578 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 50 4.0247E+02 4.4363E-01 9.8873E+00 CD 405 BOND = 22.2454 ANGLE = 108.0481 DIHED = 600.8709 VDWAALS = -409.1155 EEL = -339.0222 HBOND = 0.0000 1-4 VDW = 209.0360 1-4 EEL = 207.2432 RESTRAINT = 3.1638 EAMBER = 399.3060 NSTEP ENERGY RMS GMAX NAME NUMBER 100 3.9905E+02 6.3298E-01 1.3058E+01 CD 405 BOND = 22.2662 ANGLE = 107.9506 DIHED = 598.7822 VDWAALS = -410.3480 EEL = -339.0668 HBOND = 0.0000 1-4 VDW = 208.6463 1-4 EEL = 207.2238 RESTRAINT = 3.5925 EAMBER = 395.4543 NSTEP ENERGY RMS GMAX NAME NUMBER 150 3.9581E+02 3.6626E-01 8.8130E+00 CG 34 BOND = 22.1315 ANGLE = 108.1180 DIHED = 596.8840 VDWAALS = -411.3141 EEL = -339.1053 HBOND = 0.0000 1-4 VDW = 208.1974 1-4 EEL = 207.1919 RESTRAINT = 3.7051 EAMBER = 392.1034 NSTEP ENERGY RMS GMAX NAME NUMBER 200 3.9296E+02 5.4130E-01 1.6239E+01 CG 34 BOND = 22.1312 ANGLE = 108.3480 DIHED = 595.0296 VDWAALS = -412.1567 EEL = -339.1548 HBOND = 0.0000 1-4 VDW = 207.8165 1-4 EEL = 207.1749 RESTRAINT = 3.7667 EAMBER = 389.1887 NSTEP ENERGY RMS GMAX NAME NUMBER 250 3.9009E+02 1.6704E-01 1.1338E+00 OD2 616 BOND = 22.1008 ANGLE = 108.4442 DIHED = 593.1710 VDWAALS = -412.9450 EEL = -339.1998 HBOND = 0.0000 1-4 VDW = 207.5314 1-4 EEL = 207.1706 RESTRAINT = 3.8200 EAMBER = 386.2733 NSTEP ENERGY RMS GMAX NAME NUMBER 300 3.8740E+02 4.1209E-01 5.4244E+00 CZ 457 BOND = 22.2225 ANGLE = 108.5878 DIHED = 591.2377 VDWAALS = -413.7258 EEL = -339.2445 HBOND = 0.0000 1-4 VDW = 207.2809 1-4 EEL = 207.1656 RESTRAINT = 3.8748 EAMBER = 383.5242 NSTEP ENERGY RMS GMAX NAME NUMBER 350 3.8495E+02 5.9863E-01 8.2856E+00 CG 388 BOND = 22.2366 ANGLE = 108.8810 DIHED = 589.4107 VDWAALS = -414.4246 EEL = -339.3059 HBOND = 0.0000 1-4 VDW = 207.0483 1-4 EEL = 207.1750 RESTRAINT = 3.9248 EAMBER = 381.0210 NSTEP ENERGY RMS GMAX NAME NUMBER 400 3.8246E+02 2.2724E-01 3.4504E+00 CG 388 BOND = 21.9428 ANGLE = 109.2096 DIHED = 587.7037 VDWAALS = -415.0260 EEL = -339.3591 HBOND = 0.0000 1-4 VDW = 206.8481 1-4 EEL = 207.1688 RESTRAINT = 3.9691 EAMBER = 378.4879 NSTEP ENERGY RMS GMAX NAME NUMBER 450 3.8042E+02 5.1448E-01 9.9506E+00 CG 388 BOND = 21.9622 ANGLE = 109.4417 DIHED = 586.1242 VDWAALS = -415.5909 EEL = -339.3996 HBOND = 0.0000 1-4 VDW = 206.7055 1-4 EEL = 207.1664 RESTRAINT = 4.0131 EAMBER = 376.4095 NSTEP ENERGY RMS GMAX NAME NUMBER 500 3.7835E+02 1.7355E-01 2.2201E+00 CG 388 BOND = 21.8533 ANGLE = 109.6488 DIHED = 584.6342 VDWAALS = -416.1411 EEL = -339.4577 HBOND = 0.0000 1-4 VDW = 206.5594 1-4 EEL = 207.1943 RESTRAINT = 4.0553 EAMBER = 374.2913 NSTEP ENERGY RMS GMAX NAME NUMBER 550 3.6151E+02 4.1805E-01 5.6157E+00 CG2 9 BOND = 21.1170 ANGLE = 107.4602 DIHED = 576.7019 VDWAALS = -421.6827 EEL = -340.8735 HBOND = 0.0000 1-4 VDW = 206.2892 1-4 EEL = 207.8739 RESTRAINT = 4.6232 EAMBER = 356.8860 NSTEP ENERGY RMS GMAX NAME NUMBER 600 3.5803E+02 2.9541E-01 3.8011E+00 CA 5 BOND = 21.2266 ANGLE = 109.2540 DIHED = 572.7755 VDWAALS = -422.5014 EEL = -340.5851 HBOND = 0.0000 1-4 VDW = 205.4451 1-4 EEL = 207.7775 RESTRAINT = 4.6420 EAMBER = 353.3921 NSTEP ENERGY RMS GMAX NAME NUMBER 650 3.5619E+02 3.1288E-01 4.0653E+00 N 1 BOND = 21.1916 ANGLE = 109.6571 DIHED = 571.2962 VDWAALS = -423.1668 EEL = -340.6322 HBOND = 0.0000 1-4 VDW = 205.2868 1-4 EEL = 207.8834 RESTRAINT = 4.6739 EAMBER = 351.5161 NSTEP ENERGY RMS GMAX NAME NUMBER 700 3.5457E+02 3.6456E-01 5.6285E+00 CA 5 BOND = 21.2102 ANGLE = 109.6711 DIHED = 570.3131 VDWAALS = -423.9071 EEL = -340.6140 HBOND = 0.0000 1-4 VDW = 205.2090 1-4 EEL = 207.9685 RESTRAINT = 4.7147 EAMBER = 349.8508 NSTEP ENERGY RMS GMAX NAME NUMBER 750 3.5227E+02 5.0213E-01 4.8631E+00 N 17 BOND = 21.4783 ANGLE = 110.0601 DIHED = 568.1049 VDWAALS = -424.8541 EEL = -340.4331 HBOND = 0.0000 1-4 VDW = 204.9936 1-4 EEL = 208.1543 RESTRAINT = 4.7634 EAMBER = 347.5040 NSTEP ENERGY RMS GMAX NAME NUMBER 800 3.4933E+02 5.1259E-01 5.3205E+00 CD 420 BOND = 21.7936 ANGLE = 110.1398 DIHED = 565.3970 VDWAALS = -426.2081 EEL = -339.8297 HBOND = 0.0000 1-4 VDW = 204.9888 1-4 EEL = 208.1240 RESTRAINT = 4.9235 EAMBER = 344.4053 NSTEP ENERGY RMS GMAX NAME NUMBER 850 3.4598E+02 3.9570E-01 4.3974E+00 CB 31 BOND = 21.7161 ANGLE = 110.1614 DIHED = 561.8627 VDWAALS = -426.7029 EEL = -339.6648 HBOND = 0.0000 1-4 VDW = 205.6161 1-4 EEL = 208.0666 RESTRAINT = 4.9227 EAMBER = 341.0552 NSTEP ENERGY RMS GMAX NAME NUMBER 900 3.4437E+02 1.9564E-01 1.3197E+00 CB 7 BOND = 21.7756 ANGLE = 110.2476 DIHED = 560.8267 VDWAALS = -427.1383 EEL = -339.8592 HBOND = 0.0000 1-4 VDW = 205.3164 1-4 EEL = 208.1334 RESTRAINT = 5.0634 EAMBER = 339.3022 NSTEP ENERGY RMS GMAX NAME NUMBER 950 3.4369E+02 1.8796E-01 1.5867E+00 CA 5 BOND = 21.7728 ANGLE = 110.1749 DIHED = 560.4574 VDWAALS = -427.2564 EEL = -339.7972 HBOND = 0.0000 1-4 VDW = 205.2991 1-4 EEL = 208.0660 RESTRAINT = 4.9722 EAMBER = 338.7166 NSTEP ENERGY RMS GMAX NAME NUMBER 1000 3.4319E+02 2.0496E-01 2.3904E+00 CA 19 BOND = 21.7519 ANGLE = 110.3015 DIHED = 560.1363 VDWAALS = -427.4814 EEL = -339.8666 HBOND = 0.0000 1-4 VDW = 205.2740 1-4 EEL = 208.0716 RESTRAINT = 5.0003 EAMBER = 338.1872 MAXIMUM NUMBER OF F EVALUATION EXCEEDED FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1000 3.4319E+02 2.0496E-01 2.3904E+00 CA 19 BOND = 21.7519 ANGLE = 110.3015 DIHED = 560.1363 VDWAALS = -427.4814 EEL = -339.8666 HBOND = 0.0000 1-4 VDW = 205.2740 1-4 EEL = 208.0716 RESTRAINT = 5.0003 EAMBER = 338.1872 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Ewald setup time 0.01 ( 8.33% of List ) | Grid image cell 0.01 ( 8.33% of List ) | Build the list 0.10 (83.33% of List ) | List time 0.12 ( 0.14% of Nonbo) | Direct Ewald time 84.84 (99.00% of Ewald) | Finish NB virial 0.07 ( 0.08% of Ewald) | Other 0.79 ( 0.92% of Ewald) | Ewald time 85.70 (99.86% of Nonbo) | Nonbond force 85.82 (93.36% of Force) | Bond energy 0.10 ( 0.11% of Force) | Angle energy 1.39 ( 1.51% of Force) | Dihedral energy 4.45 ( 4.84% of Force) | Other 0.16 ( 0.17% of Force) | Force time 91.92 (100.0% of Runmd) | Runmd Time 91.92 (99.24% of Total) | Other 0.70 ( 0.76% of Total) | Total time 92.62 (100.0% of ALL ) | Highest rstack allocated: 4665 | Highest istack allocated: 56552 | Setup wallclock 0 seconds | Nonsetup wallclock 95 seconds