------------------------------------------------------- Amber 7 SANDER Scripps/UCSF 2002 ------------------------------------------------------- | Sun Feb 24 00:00:56 2002 [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: trx.min.out |INPCRD: trx.crd | PARM: trx.top |RESTRT: trx.rst | REFC: trx.crd | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: mimimize structure &cntrl imin=1, maxcyc=100, cut=300.0, igb=2, saltcon=0.2, gbsa=1, ntpr=10, ntx=1, ntb=0, ntr=1, &end keep all atoms frozen 5.0 RES 1 108 END END -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 02/21/02 Time = 19:40:40 NATOM = 1654 NTYPES = 14 NBONH = 832 MBONA = 838 NTHETH = 1911 MTHETA = 1138 NPHIH = 3535 MPHIA = 2155 NHPARM = 0 NPARM = 0 NNB = 9195 NRES = 108 NBONA = 838 NTHETA = 1138 NPHIA = 2155 NUMBND = 42 NUMANG = 91 NPTRA = 42 NATYP = 27 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 | Memory Use Allocated Used | Real 2000000 76273 | Hollerith 400000 10034 | Integer 2000000 157178 | 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 = 2, nsnb = 25 ipol = 0, gbsa = 1 dielc = 1.00000, cut = 300.00000, intdiel = 1.00000 saltcon = 0.20000, offset = 0.09000, gbalpha= 0.80000 gbbeta = 0.00000, gbgamma = 2.90912, surften = 0.00500 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 1 Energy minimization: maxcyc = 100, ncyc = 10, 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: keep all atoms frozen GROUP 1 HAS HARMONIC CONSTRAINTS 5.00000 GRP 1 RES 1 TO 108 Number of atoms in this group = 1654 ----- 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 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NSTEP ENERGY RMS GMAX NAME NUMBER 1 -2.6695E+03 1.4295E+01 1.6593E+02 HD3 1020 BOND = 158.2876 ANGLE = 333.3177 DIHED = 926.6942 VDWAALS = -735.5748 EEL = -8283.6186 EGB = -1699.1415 1-4 VDW = 487.5186 1-4 EEL = 6115.6341 RESTRAINT = 0.0000 ESURF = 27.3360 NSTEP ENERGY RMS GMAX NAME NUMBER 10 -2.8571E+03 7.5334E+00 7.9870E+01 HD3 1020 BOND = 66.1394 ANGLE = 270.8638 DIHED = 924.4035 VDWAALS = -754.9079 EEL = -8280.6820 EGB = -1698.6464 1-4 VDW = 480.8372 1-4 EEL = 6107.2186 RESTRAINT = 0.3088 ESURF = 27.3607 EAMBER = -2857.4131 NSTEP ENERGY RMS GMAX NAME NUMBER 20 -3.1450E+03 3.2624E+00 3.7007E+01 CD 1308 BOND = 32.4160 ANGLE = 180.3698 DIHED = 923.1773 VDWAALS = -827.1467 EEL = -8247.7372 EGB = -1707.2353 1-4 VDW = 423.3016 1-4 EEL = 6036.9702 RESTRAINT = 13.7239 ESURF = 27.1533 EAMBER = -3158.7309 NSTEP ENERGY RMS GMAX NAME NUMBER 30 -3.1985E+03 1.6078E+00 1.2100E+01 HB1 1012 BOND = 34.8327 ANGLE = 164.2800 DIHED = 920.0447 VDWAALS = -835.7482 EEL = -8234.8496 EGB = -1708.9924 1-4 VDW = 397.6173 1-4 EEL = 6014.0884 RESTRAINT = 23.1727 ESURF = 27.0870 EAMBER = -3221.6401 NSTEP ENERGY RMS GMAX NAME NUMBER 40 -3.2354E+03 1.6250E+00 1.0753E+01 OE2 726 BOND = 35.1313 ANGLE = 157.6897 DIHED = 917.0593 VDWAALS = -851.4667 EEL = -8209.6237 EGB = -1714.5306 1-4 VDW = 377.4217 1-4 EEL = 5986.7999 RESTRAINT = 39.0945 ESURF = 27.0422 EAMBER = -3274.4770 NSTEP ENERGY RMS GMAX NAME NUMBER 50 -3.2486E+03 5.8903E-01 7.2225E+00 CD 1308 BOND = 37.4396 ANGLE = 162.2221 DIHED = 917.5852 VDWAALS = -861.4299 EEL = -8198.2282 EGB = -1716.3633 1-4 VDW = 363.3658 1-4 EEL = 5965.7468 RESTRAINT = 54.0477 ESURF = 27.0152 EAMBER = -3302.6467 NSTEP ENERGY RMS GMAX NAME NUMBER 60 -3.2502E+03 4.5352E-01 4.9816E+00 CD 1308 BOND = 36.8778 ANGLE = 160.6323 DIHED = 916.5088 VDWAALS = -861.6444 EEL = -8199.6551 EGB = -1716.9164 1-4 VDW = 365.3098 1-4 EEL = 5967.7019 RESTRAINT = 53.9382 ESURF = 27.0313 EAMBER = -3304.1541 NSTEP ENERGY RMS GMAX NAME NUMBER 70 -3.2530E+03 3.4395E-01 3.3618E+00 CD 724 BOND = 35.8274 ANGLE = 158.1959 DIHED = 914.0944 VDWAALS = -862.2848 EEL = -8201.5459 EGB = -1716.5981 1-4 VDW = 366.9638 1-4 EEL = 5968.0514 RESTRAINT = 57.2326 ESURF = 27.0556 EAMBER = -3310.2402 NSTEP ENERGY RMS GMAX NAME NUMBER 80 -3.2520E+03 1.2725E+00 1.4001E+01 CD 724 BOND = 36.5812 ANGLE = 159.6990 DIHED = 913.7408 VDWAALS = -863.8178 EEL = -8200.9135 EGB = -1716.2243 1-4 VDW = 365.1712 1-4 EEL = 5965.7712 RESTRAINT = 60.9746 ESURF = 27.0587 EAMBER = -3312.9336 NSTEP ENERGY RMS GMAX NAME NUMBER 90 -3.2543E+03 1.8893E-01 1.4647E+00 OE2 726 BOND = 36.5623 ANGLE = 158.5796 DIHED = 913.4833 VDWAALS = -863.8214 EEL = -8200.6038 EGB = -1716.6583 1-4 VDW = 364.0512 1-4 EEL = 5964.6949 RESTRAINT = 62.4074 ESURF = 27.0505 EAMBER = -3316.6617 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -3.2544E+03 1.0010E-01 9.8816E-01 CD 1308 BOND = 36.6220 ANGLE = 159.0088 DIHED = 913.3132 VDWAALS = -864.0395 EEL = -8200.8472 EGB = -1716.4795 1-4 VDW = 363.5903 1-4 EEL = 5964.0759 RESTRAINT = 63.2982 ESURF = 27.0432 EAMBER = -3317.7128 MAXIMUM NUMBER OF F EVALUATION EXCEEDED FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 100 -3.2544E+03 1.0010E-01 9.8816E-01 CD 1308 BOND = 36.6220 ANGLE = 159.0088 DIHED = 913.3132 VDWAALS = -864.0395 EEL = -8200.8472 EGB = -1716.4795 1-4 VDW = 363.5903 1-4 EEL = 5964.0759 RESTRAINT = 63.2982 ESURF = 27.0432 EAMBER = -3317.7128 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 228.96 (19.87% of Gen B) | Calc gb diag 516.01 (44.78% of Gen B) | Calc gb off-diag 343.69 (29.83% of Gen B) | Surface area energy 63.62 ( 5.52% of Gen B) | Gen Born time 1152.28 (100.0% of Nonbo) | Nonbond force 1152.28 (99.58% of Force) | Bond energy 0.09 ( 0.01% of Force) | Angle energy 0.77 ( 0.07% of Force) | Dihedral energy 4.04 ( 0.35% of Force) | Force time 1157.18 (100.0% of Runmd) | Runmd Time 1157.18 (100.0% of Total) | Total time 1094.86 (100.0% of ALL ) | Highest rstack allocated: 18194 | Highest istack allocated: 6616 | Setup wallclock 1 seconds | Nonsetup wallclock 1126 seconds