------------------------------------------------------ Amber 4.1 (SANDER, double precision) Scripps/UCSF 1993 ------------------------------------------------------ [-O]verwriting output File Assignments: |MDIN : min.in |MDOUT: min.out |INPCR: stbtcap.crd |PARM : stbtcap.top |RESTR: min.rst |REFC : refc |MDVEL: mdvel |MDEN : mden |MDCRD: mdcrd |MDINF: mdinfo Here is the input file: &cntrl imin=1, maxcyc=100, ntpr=20, scee=1.2, nsnb=999999, ntmin=2, &end ------------------------------------------------------------------------------- | Reading &cntrl namelist w/ portable lib 1. R E S O U R C E U S E NATOM = 7831 NTYPES = 16 NBONH = 4215 MBONA = 3708 NTHETH = 7560 MTHETA = 5080 NPHIH = 13956 MPHIA = 8912 NHPARM = 0 NPARM = 0 NNB = 39344 NRES = 757 NBONA = 3708 NTHETA = 5080 NPHIA = 8912 NUMBND = 43 NUMANG = 89 NPTRA = 32 NATYP = 29 NPHB = 1 IFBOX = 0 NMXRS = 31 IFCAP = 1 | Memory Use Allocated Used | Real 2000000 524812 | Hollerith 300000 180872 | Integer 800000 403851 (static) | Max Nonbonded Pairs: 5000000 packed 2 to a machine word %MINMD/POL-I-CAP_INFO, cap option on: NATCAP = 7000 CUTCAP = 20.000 XYZCAP = 35.000 12.000 -6.000 2. C O N T R O L D A T A F O R T H E R U N TIMLIM= 999999. IREST = 0 IBELLY= 0 KFORM = 1 ICHDNA= 0 IMIN = 1 IPOL = 0 IEWALD= 0 NTX = 1 NTXO = 1 IG = 71277 TEMPI = .00 HEAT = .000 NTB = 0 IFTRES= 1 BOXX = .000 BOXY = .000 BOXZ = .000 BETA = .000 NRUN = 1 NTT = 0 TEMP0 = 300.000 DTEMP = .000 TAUTP = .200 TAUTS = .200 ISOLVP= 0 VLIMIT= .000 NTP = 0 PRES0 = 1.000 COMP = 44.600 TAUP = .200 NPSCAL= 0 NTCM = 0 NSCM = 9999999 NSTLIM= 1 INIT = 3 NTU = 1 T = .000 DT = .00100 NTC = 1 TOL = .00050 JFASTW = 0 NTF = 1 NTID = 0 NTNB = 1 NSNB =***** IDIEL = 1 IMGSLT= 0 IPRR = 0 IPRW = 0 CUT = 8.000 SCNB = 2.000 SCEE = 1.200 DIELC = 1.000 CUT2ND= .00000 NTPR = 20 NTWX = 0 NTWV = 0 NTWE = 0 NTWXM = 999999 NTWVM = 999999 NTWEM = 999999 IOUTFM= 0 NTWPRT= 0 NTWPR0= 0 NTR = 0 NTRX = 1 TAUR = .00000 NMRMAX= 0 ISFTRP= 0 RWELL = 1.00000 PENCUT= .10000 IVCAP = 0 MATCAP= 0 FCAP = 1.500 OTHER DATA: IFCAP = 1 NATCAP= 7000 CUTCAP= 20.000 XCAP = 35.000 YCAP = 12.000 ZCAP = -6.000 NATOM = 7831 NRES = 757 MAXCYC= 100 NCYC = 10 NTMIN = 2 DX0 = .010000 DXM = .50000 DRMS = .00010 Water definition for fast triangulated model: Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ; Hyd2_name = H2 3. ATOMIC COORDINATES AND VELOCITIES begin time read from input coords = .000 ps Number of triangulated 3-point waters found: 277 Using 277 waters for fast wat-wat Solute/solvent pointers: IPTSOL= 757 NATRCM= 7831 IPTRES= 0 IPTATM= 0 NSPSOL= 0 NSPSTR= 0 NSOLUT= 7831 NATOM = 7831 NB-update: NPAIRS = 1938810 HBPAIR = 21240 NSTEP ENERGY RMS GMAX NAME NUMBER 1 1.8293E+04 1.7620E+03 1.2900E+05 HE1 5266 BOND = 946.8923 ANGLE = 3567.9338 DIHED = 2339.0414 VDWAALS = 18866.3356 EEL = -35181.6669 HBOND = .0000 1-4 VDW = 7659.1317 1-4 EEL = 20095.1911 CONSTRAINT = .0000 EPOLAR = .0000 ETHREEB = .0000 NSTEP ENERGY RMS GMAX NAME NUMBER 20 -7.9463E+03 2.8552E+01 7.9692E+02 HG 3772 BOND = 886.2550 ANGLE = 3445.8906 DIHED = 2333.6449 VDWAALS = -2817.2975 EEL = -35208.1145 HBOND = .0000 1-4 VDW = 3323.5129 1-4 EEL = 20089.7803 CONSTRAINT = .0000 EPOLAR = .0000 ETHREEB = .0000 NSTEP ENERGY RMS GMAX NAME NUMBER 40 -1.4693E+04 3.6013E+00 9.7082E+01 C1 6909 BOND = 349.2322 ANGLE = 1140.8757 DIHED = 2257.7045 VDWAALS = -3729.4336 EEL = -35990.9067 HBOND = .0000 1-4 VDW = 1643.2260 1-4 EEL = 19636.6744 CONSTRAINT = .0000 EPOLAR = .0000 ETHREEB = .0000 NSTEP ENERGY RMS GMAX NAME NUMBER 60 -1.5235E+04 1.4210E+00 2.5044E+01 H2 7477 BOND = 318.5429 ANGLE = 1068.3532 DIHED = 2270.9483 VDWAALS = -3769.9043 EEL = -36239.5633 HBOND = .0000 1-4 VDW = 1567.4223 1-4 EEL = 19548.8495 CONSTRAINT = .0000 EPOLAR = .0000 ETHREEB = .0000 NSTEP ENERGY RMS GMAX NAME NUMBER 80 -1.5541E+04 2.0192E+00 2.4961E+01 HB2 3769 BOND = 337.4287 ANGLE = 1009.1709 DIHED = 2286.0107 VDWAALS = -3783.2309 EEL = -36411.7061 HBOND = .0000 1-4 VDW = 1522.4721 1-4 EEL = 19499.0746 CONSTRAINT = .0000 EPOLAR = .0000 ETHREEB = .0000 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -1.5784E+04 2.7151E+00 1.0090E+02 C1 6971 BOND = 359.9258 ANGLE = 937.4715 DIHED = 2301.4923 VDWAALS = -3786.7471 EEL = -36547.4522 HBOND = .0000 1-4 VDW = 1485.3488 1-4 EEL = 19465.8751 CONSTRAINT = .0000 EPOLAR = .0000 ETHREEB = .0000 MAXIMUM NUMBER OF F EVALUATION EXCEEDED FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 100 -1.5784E+04 2.7151E+00 1.0090E+02 C1 6971 BOND = 359.9258 ANGLE = 937.4715 DIHED = 2301.4923 VDWAALS = -3786.7471 EEL = -36547.4522 HBOND = .0000 1-4 VDW = 1485.3488 1-4 EEL = 19465.8751 CONSTRAINT = .0000 EPOLAR = .0000 ETHREEB = .0000 | ELAPSED TIME = 206.150 TOTAL TIME = 206.150 Routine Sec % ---------------------------- | Pairlist 9.97 4.84 | Nonbond 137.65 66.77 | Bond 1.35 .65 | Angle 6.28 3.05 | Dihedral 42.73 20.73 | Shake .00 .00 | Quick3 .00 .00 | Force .00 .00 | Other 8.17 3.96 ---------------------------- | Total 206.15 .06 Hours | Nonsetup 200.81 97.41% | Setup wallclock 9 seconds | Nonsetup wallclock 216 seconds