------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 11/12/2009 at 20:57:18 [-O]verwriting output File Assignments: | MDIN: minvac.in | MDOUT: DRUG0minvac.out |INPCRD: DRUG0.crd | PARM: DRUG0.top |RESTRT: DRUG0minvac.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 = 11/12/09 Time = 20:56:51 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 2.3986E+13 5.4709E+13 4.1164E+15 H 1574 BOND = 1462.0449 ANGLE = 3684.0927 DIHED = 2438.5216 VDWAALS = ************* EEL = -16015.8019 EGB = -4636.8712 1-4 VDW = 10990577.4004 1-4 EEL = 11440.2810 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 50 3.2881E+03 1.5564E+01 7.3743E+02 C24 3959 BOND = 2499.1062 ANGLE = 3152.1964 DIHED = 2973.1015 VDWAALS = 2181.4277 EEL = -15947.2873 EGB = -4647.3603 1-4 VDW = 2142.5273 1-4 EEL = 10934.3844 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -4.7754E+03 8.3233E+00 5.4211E+02 C23 3966 BOND = 453.1051 ANGLE = 1312.3278 DIHED = 2710.9937 VDWAALS = -533.1956 EEL = -15636.3904 EGB = -4801.6196 1-4 VDW = 1293.4904 1-4 EEL = 10425.8663 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 150 -6.3033E+03 5.4729E+00 4.3593E+02 C23 3966 BOND = 290.6248 ANGLE = 979.3447 DIHED = 2602.0784 VDWAALS = -1064.1850 EEL = -15569.7313 EGB = -4884.9606 1-4 VDW = 1076.8793 1-4 EEL = 10266.6925 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -1.2306E+05 1.5163E+06 9.5849E+07 O13 3933 BOND = 252.9692 ANGLE = 980.3891 DIHED = 2575.3666 VDWAALS = -1168.7465 EEL = -15553.3348 EGB = -4999.3962 1-4 VDW = 1026.0943 1-4 EEL = -106171.5284 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 250 -1.2410E+08 1.7209E+12 1.0879E+14 H40 3932 BOND = 253.0053 ANGLE = 980.4497 DIHED = 2575.3680 VDWAALS = -1168.7094 EEL = -15553.3400 EGB = -4999.4200 1-4 VDW = 1026.0942 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 300 -1.9493E+08 4.2459E+12 2.6840E+14 H40 3932 BOND = 253.0053 ANGLE = 980.4497 DIHED = 2575.3680 VDWAALS = -1168.7094 EEL = -15553.3400 EGB = -4999.4200 1-4 VDW = 1026.0942 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 350 -4.8350E+07 2.6117E+11 1.6510E+13 H40 3932 BOND = 253.0054 ANGLE = 980.4498 DIHED = 2575.3680 VDWAALS = -1168.7093 EEL = -15553.3400 EGB = -4999.4200 1-4 VDW = 1026.0942 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 400 -1.2410E+08 1.7209E+12 1.0879E+14 H40 3932 BOND = 253.0053 ANGLE = 980.4497 DIHED = 2575.3680 VDWAALS = -1168.7094 EEL = -15553.3400 EGB = -4999.4200 1-4 VDW = 1026.0942 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 450 -1.9493E+08 4.2459E+12 2.6840E+14 H40 3932 BOND = 253.0053 ANGLE = 980.4497 DIHED = 2575.3680 VDWAALS = -1168.7094 EEL = -15553.3400 EGB = -4999.4200 1-4 VDW = 1026.0942 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 500 -4.8350E+07 2.6117E+11 1.6510E+13 H40 3932 BOND = 253.0054 ANGLE = 980.4498 DIHED = 2575.3680 VDWAALS = -1168.7093 EEL = -15553.3400 EGB = -4999.4200 1-4 VDW = 1026.0942 1-4 EEL = ************* RESTRAINT = 0.0000 .... RESTARTED DUE TO LINMIN FAILURE ... NSTEP ENERGY RMS GMAX NAME NUMBER 550 2.6385E+12 9.3394E+05 4.5191E+07 C17 3946 BOND = ************* ANGLE = 8929.3990 DIHED = 2612.2735 VDWAALS = -1260.9869 EEL = -15887.8959 EGB = -6465.7338 1-4 VDW = 969.4188 1-4 EEL = 11420.0719 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 600 2.6013E+09 1.0831E+04 3.9215E+05 C23 3966 BOND = ************* ANGLE = 7338.3612 DIHED = 2493.9110 VDWAALS = -1126.4913 EEL = -16092.3047 EGB = -6771.2385 1-4 VDW = 903.4826 1-4 EEL = 11619.4636 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 650 2.4721E+09 1.1227E+07 6.2147E+08 ND1 2030 BOND = ************* ANGLE = 24638.1076 DIHED = 2770.2325 VDWAALS = 52641945.5252 EEL = -15645.9778 EGB = -7254.9345 1-4 VDW = 2216.3741 1-4 EEL = 11294.2259 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 700 2.3281E+09 5.1419E+05 3.7907E+07 CD2 2035 BOND = ************* ANGLE = 30618.5449 DIHED = 2986.0508 VDWAALS = 3727444.7286 EEL = -15423.6645 EGB = -7196.6263 1-4 VDW = 2339.2001 1-4 EEL = 10574.2986 RESTRAINT = 0.0000 .... RESTARTED DUE TO LINMIN FAILURE ... NSTEP ENERGY RMS GMAX NAME NUMBER 750 1.2331E+18 8.2260E+08 3.8823E+10 CB 2131 BOND = ************* ANGLE = 73661.5744 DIHED = 3537.7051 VDWAALS = ************* EEL = -14306.2838 EGB = -8898.0497 1-4 VDW = 21191.4715 1-4 EEL = 10387.3376 RESTRAINT = 0.0000 .... RESTARTED DUE TO LINMIN FAILURE ... NSTEP ENERGY RMS GMAX NAME NUMBER 800 9.2645E+16 1.4163E+09 8.2787E+10 CD1 2136 BOND = ************* ANGLE = 84114.0186 DIHED = 4016.2701 VDWAALS = ************* EEL = -14374.5288 EGB = -9653.6709 1-4 VDW = 2573528.8033 1-4 EEL = 10263.4323 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 850 1.2902E+16 4.3993E+07 1.1756E+09 CG2 1988 BOND = ************* ANGLE = 173281.9339 DIHED = 4763.7019 VDWAALS = 16603281.4982 EEL = -10303.2756 EGB = -16142.9812 1-4 VDW = 6368447.2798 1-4 EEL = 7788.7054 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 900 5.5132E+15 4.2725E+10 3.2855E+12 CB 1813 BOND = ************* ANGLE = 300549.1228 DIHED = 5504.8157 VDWAALS = ************* EEL = -6683.4492 EGB = -25124.4255 1-4 VDW = ************* 1-4 EEL = 5233.8140 RESTRAINT = 0.0000 .... 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 934 1.4066E+30 6.4826E+14 3.1597E+16 CA 1618 BOND = ************* ANGLE = 634473.0931 DIHED = 9271.6949 VDWAALS = -0.0000 EEL = -0.0360 EGB = -51523.6366 1-4 VDW = -0.0000 1-4 EEL = 0.3884 RESTRAINT = 0.0000 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 500.24 (15.65% of Gen B) | Calc gb diag 926.83 (29.00% of Gen B) | Calc gb off-diag 1768.86 (55.35% of Gen B) | Gen Born time 3195.94 (100.0% of Nonbo) | Nonbond force 3195.94 (99.54% of Force) | Bond/Angle/Dihedral 14.67 ( 0.46% of Force) | Force time 3210.63 (100.0% of Runmd) | Runmd Time 3210.63 (100.0% of Total) | Other 0.57 ( 0.02% of Total) | Total time 3211.21 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 20:57:18.236 on 11/12/2009 | Setup done at 20:57:18.332 on 11/12/2009 | Run done at 21:50:49.447 on 11/12/2009 | wallclock() was called 16820 times