------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 03/13/2010 at 02:01:36 [-O]verwriting output File Assignments: | MDIN: minvac.in | MDOUT: DRUG7minvac.out |INPCRD: DRUG7.crd | PARM: DRUG7.top |RESTRT: DRUG7minvac.crd | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: in vacuo minimization &cntrl imin = 1, maxcyc = 1000, ncyc = 500, ntb = 0, igb = 5, cut = 999 / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 03/12/10 Time = 19:09:19 NATOM = 3967 NTYPES = 17 NBONH = 2026 MBONA = 1969 NTHETH = 4610 MTHETA = 2652 NPHIH = 8657 MPHIA = 5238 NHPARM = 0 NPARM = 0 NNB = 21966 NRES = 241 NBONA = 1969 NTHETA = 2652 NPHIA = 5238 NUMBND = 55 NUMANG = 110 NPTRA = 46 NATYP = 42 NPHB = 0 IFBOX = 0 NMXRS = 40 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 254409 | Hollerith 24045 | Integer 218908 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 2936 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 = 5, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00500 rdt = 0.00000, rgbmax = 25.00000 alpb = 0 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 1000, ncyc = 500, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file 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 5.4905E+08 1.4970E+08 8.7095E+09 CB 1897 BOND = 117.5665 ANGLE = 723.4817 DIHED = 2152.1055 VDWAALS = ************* EEL = -15974.7859 EGB = -3955.9543 1-4 VDW = 875.2768 1-4 EEL = 10425.8741 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 50 -1.1374E+04 1.5979E+03 1.0052E+05 O13 3933 BOND = 232.2030 ANGLE = 768.6140 DIHED = 2149.1236 VDWAALS = -1831.2067 EEL = -15982.2737 EGB = -4081.1604 1-4 VDW = 861.5045 1-4 EEL = 6509.3210 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -1.4038E+07 2.1997E+10 1.3830E+12 H40 3932 BOND = 232.1475 ANGLE = 768.2889 DIHED = 2149.0765 VDWAALS = -1832.1348 EEL = -15982.4181 EGB = -4081.1276 1-4 VDW = 861.5028 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 150 -1.5744E+08 2.7698E+12 1.7414E+14 H40 3932 BOND = 232.1475 ANGLE = 768.2889 DIHED = 2149.0765 VDWAALS = -1832.1345 EEL = -15982.4180 EGB = -4081.1276 1-4 VDW = 861.5028 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -2.9209E+08 9.5334E+12 5.9938E+14 H40 3932 BOND = 232.1475 ANGLE = 768.2889 DIHED = 2149.0765 VDWAALS = -1832.1345 EEL = -15982.4180 EGB = -4081.1276 1-4 VDW = 861.5028 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 250 -5.2698E+07 3.1025E+11 1.9506E+13 H40 3932 BOND = 232.1475 ANGLE = 768.2889 DIHED = 2149.0765 VDWAALS = -1832.1346 EEL = -15982.4180 EGB = -4081.1276 1-4 VDW = 861.5028 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 300 -1.5744E+08 2.7698E+12 1.7414E+14 H40 3932 BOND = 232.1475 ANGLE = 768.2889 DIHED = 2149.0765 VDWAALS = -1832.1345 EEL = -15982.4180 EGB = -4081.1276 1-4 VDW = 861.5028 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 350 -2.9209E+08 9.5334E+12 5.9938E+14 H40 3932 BOND = 232.1475 ANGLE = 768.2889 DIHED = 2149.0765 VDWAALS = -1832.1345 EEL = -15982.4180 EGB = -4081.1276 1-4 VDW = 861.5028 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 400 -5.2698E+07 3.1025E+11 1.9506E+13 H40 3932 BOND = 232.1475 ANGLE = 768.2889 DIHED = 2149.0765 VDWAALS = -1832.1346 EEL = -15982.4180 EGB = -4081.1276 1-4 VDW = 861.5028 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 450 -1.5744E+08 2.7698E+12 1.7414E+14 H40 3932 BOND = 232.1475 ANGLE = 768.2889 DIHED = 2149.0765 VDWAALS = -1832.1345 EEL = -15982.4180 EGB = -4081.1276 1-4 VDW = 861.5028 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 500 -2.9209E+08 9.5334E+12 5.9938E+14 H40 3932 BOND = 232.1475 ANGLE = 768.2889 DIHED = 2149.0765 VDWAALS = -1832.1345 EEL = -15982.4180 EGB = -4081.1276 1-4 VDW = 861.5028 1-4 EEL = ************* RESTRAINT = 0.0000 .... RESTARTED DUE TO LINMIN FAILURE ... NSTEP ENERGY RMS GMAX NAME NUMBER 550 1.2564E+19 1.0775E+09 4.5549E+10 C18 3950 BOND = ************* ANGLE = 9644.3107 DIHED = 2214.1477 VDWAALS = -2013.5526 EEL = -16633.6916 EGB = -5574.3044 1-4 VDW = 829.1946 1-4 EEL = 11413.2957 RESTRAINT = 0.0000 .... RESTARTED DUE TO LINMIN FAILURE ... .... RESTARTED DUE TO LINMIN FAILURE ... .... RESTARTED DUE TO LINMIN FAILURE ... .... RESTARTED DUE TO LINMIN FAILURE ... ***** REPEATED LINMIN FAILURE ***** ***** SEE http://amber.scripps.edu/Questions/linmin.html FOR MORE INFO ***** FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 594 2.9878E+17 9.2654E+07 3.4478E+09 C19 3943 BOND = ************* ANGLE = 8627.2388 DIHED = 2179.4333 VDWAALS = -2032.9453 EEL = -16600.3083 EGB = -6013.6579 1-4 VDW = 815.6767 1-4 EEL = 11567.8530 RESTRAINT = 0.0000 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 408.42 (17.64% of Gen B) | Calc gb diag 751.22 (32.44% of Gen B) | Calc gb off-diag 1156.22 (49.93% of Gen B) | Gen Born time 2315.88 (100.0% of Nonbo) | Nonbond force 2315.88 (99.60% of Force) | Bond/Angle/Dihedral 9.39 ( 0.40% of Force) | Force time 2325.27 (100.0% of Runmd) | Runmd Time 2325.27 (100.0% of Total) | Other 0.20 ( 0.01% of Total) | Total time 2325.48 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 02:01:36.001 on 03/13/2010 | Setup done at 02:01:36.072 on 03/13/2010 | Run done at 02:40:21.481 on 03/13/2010 | wallclock() was called 10700 times