------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 02/23/2004 at 16:03:36 [-O]verwriting output File Assignments: | MDIN: polyAT_vac_init_min_gb.in | MDOUT: polyAT_vac_init_min_gb.out |INPCRD: polyAT_vac.inpcrd | PARM: polyAT_vac.prmtop |RESTRT: polyAT_vac_init_min_gb.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: polyA-polyT 10-mer: initial minimisation prior to MD &cntrl imin = 1, maxcyc = 500, ncyc = 250, ntb = 0, igb = 1, cut = 12 &end -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 02/19/04 Time = 15:33:29 NATOM = 638 NTYPES = 14 NBONH = 234 MBONA = 452 NTHETH = 554 MTHETA = 694 NPHIH = 1056 MPHIA = 1238 NHPARM = 0 NPARM = 0 NNB = 3544 NRES = 20 NBONA = 452 NTHETA = 694 NPHIA = 1238 NUMBND = 32 NUMANG = 59 NPTRA = 39 NATYP = 24 NPHB = 0 IFBOX = 0 NMXRS = 33 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 23881 | Hollerith 3850 | Integer 53552 | Max Pairs 1 | Max Rstack 1 | Max Istack 1 | Total 410 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 = 1, ntb = 0, igb = 1, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 12.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500 rdt = 0.00000, rgbmax = 25.00000 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 -------------------------------------------------------------------------------- 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 -1.2532E+03 4.7970E+01 6.6837E+02 O5' 321 BOND = 929.3608 ANGLE = 544.5351 DIHED = 467.8807 VDWAALS = 150.6633 EEL = -1984.8745 EGB = -1345.2559 1-4 VDW = 264.8124 1-4 EEL = -280.3135 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 50 -3.1049E+03 1.6206E+00 1.3208E+01 O5' 321 BOND = 25.4789 ANGLE = 121.9414 DIHED = 430.2710 VDWAALS = -241.2381 EEL = -2285.7023 EGB = -961.5729 1-4 VDW = 168.8999 1-4 EEL = -362.9502 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -3.1732E+03 1.7383E+00 8.8543E+00 C4 626 BOND = 23.4724 ANGLE = 111.1648 DIHED = 417.3569 VDWAALS = -281.7706 EEL = -1786.8040 EGB = -1457.8510 1-4 VDW = 161.7621 1-4 EEL = -360.5362 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 150 -3.2069E+03 7.6161E-01 3.4500E+00 C2 502 BOND = 22.5462 ANGLE = 108.1788 DIHED = 411.5635 VDWAALS = -302.2415 EEL = -1972.2468 EGB = -1273.4093 1-4 VDW = 158.7803 1-4 EEL = -360.0222 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -3.2222E+03 5.1079E-01 2.9331E+00 H72 624 BOND = 21.6940 ANGLE = 107.5344 DIHED = 408.2869 VDWAALS = -311.9878 EEL = -1992.5165 EGB = -1251.6972 1-4 VDW = 157.1692 1-4 EEL = -360.6402 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 250 -3.2249E+03 4.9771E-01 2.8409E+00 H72 624 BOND = 21.5762 ANGLE = 107.3669 DIHED = 407.5535 VDWAALS = -314.0220 EEL = -1962.1660 EGB = -1281.2299 1-4 VDW = 156.8452 1-4 EEL = -360.8047 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 300 -3.2912E+03 7.6493E-01 4.5374E+00 C5 365 BOND = 20.5498 ANGLE = 110.8929 DIHED = 385.4819 VDWAALS = -361.5669 EEL = -1850.5887 EGB = -1379.0438 1-4 VDW = 146.8919 1-4 EEL = -363.8564 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 350 -3.2940E+03 1.1022E+00 8.0096E+00 C2 630 BOND = 20.6805 ANGLE = 107.3655 DIHED = 385.8622 VDWAALS = -360.8619 EEL = -1855.0708 EGB = -1374.6215 1-4 VDW = 146.7024 1-4 EEL = -364.0989 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 400 -3.3053E+03 1.5491E+00 1.0299E+01 O2 631 BOND = 22.8003 ANGLE = 96.1966 DIHED = 388.5218 VDWAALS = -357.0061 EEL = -2106.9961 EGB = -1134.6245 1-4 VDW = 146.1672 1-4 EEL = -360.4046 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 450 -3.3102E+03 5.0490E-01 4.7276E+00 C5 621 BOND = 20.1534 ANGLE = 94.2894 DIHED = 388.0396 VDWAALS = -357.2552 EEL = -2232.4529 EGB = -1010.5880 1-4 VDW = 147.3017 1-4 EEL = -359.7059 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 500 -3.3213E+03 6.1170E-01 3.5734E+00 C5 621 BOND = 19.8606 ANGLE = 94.8508 DIHED = 384.7276 VDWAALS = -358.2907 EEL = -2579.0355 EGB = -674.2712 1-4 VDW = 146.3847 1-4 EEL = -355.4854 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 500 -3.3213E+03 6.1170E-01 3.5734E+00 C5 621 BOND = 19.8606 ANGLE = 94.8508 DIHED = 384.7276 VDWAALS = -358.2907 EEL = -2579.0355 EGB = -674.2712 1-4 VDW = 146.3847 1-4 EEL = -355.4854 RESTRAINT = 0.0000 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 12.68 (27.07% of Gen B) | Calc gb diag 23.88 (50.97% of Gen B) | Calc gb off-diag 10.29 (21.96% of Gen B) | Other 0.00 ( 0.01% of Gen B) | Gen Born time 46.86 (100.0% of Nonbo) | Nonbond force 46.86 (98.22% of Force) | Bond/Angle/Dihedral 0.84 ( 1.77% of Force) | Other 0.00 ( 0.01% of Force) | Force time 47.70 (100.0% of Runmd) | Runmd Time 47.70 (99.64% of Total) | Other 0.17 ( 0.35% of Total) | Total time 47.88 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 16:03:36.616 on 02/23/2004 | Setup done at 16:03:36.681 on 02/23/2004 | Run done at 16:04:24.507 on 02/23/2004 | wallclock() was called 7008 times