------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 09/14/2006 at 10:41:32 [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: crambin_divcon.out |INPCRD: crambin.crd | PARM: prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Crambin: 5 cycles minimization using qm calculation &cntrl imin =1, maxcyc = 5, drms=0.005, scee=1.2, ntpr=1, ntb=0, cut=8.1, ifqnt=1, igb=6 / &qmmm iqmatoms= 80,81,82,83,84,85,86,87,88,89,90, 91,92,99,100,101,102,103,104, 105,106,107,108,115,116,117,118, 125,126,127,128,129,130,131,132,133, 134,135,136,137,138,139,140,141,142, 149,150,151,152,153, 160,161,162,163,164,165,166,167, 174,175,176,177,178,179,180,181,182, 183,184,185,186,187, 194,195,196,197,198,199,200,201, qmtheory=1,adjust_q=0, qmcharge=1, idc=2 / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 06/24/03 Time = 11:20:38 NATOM = 642 NTYPES = 12 NBONH = 315 MBONA = 334 NTHETH = 717 MTHETA = 460 NPHIH = 1277 MPHIA = 844 NHPARM = 0 NPARM = 0 NNB = 3545 NRES = 46 NBONA = 334 NTHETA = 460 NPHIA = 844 NUMBND = 23 NUMANG = 50 NPTRA = 21 NATYP = 16 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 41396 | Hollerith 3900 | Integer 51666 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 540 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals |QMMM: WARNING DIVCON IN USE |QMMM: qmtheory IS IGNORED WHEN USING DIVCON - QM HAMILTONIAN MUST BE SELECTED |QMMM: IN DIVCON.IN FILE. -------------------------------------------------------------------------------- 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 = 1, 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 = 6, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 8.10000, 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 alpb = 0 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 5, ncyc = 10, ntmin = 1 dx0 = 0.01000, drms = 0.00500 QMMM options: ifqnt = True nquant = 80 qmgb = 0 qmcharge = 1 adjust_q = 0 spin = 1 qmcut = 8.1000 qmshake = 1 lnk_atomic_no = 1 lnk_dis = 1.0900 qmtheory = PM3 verbosity = 0 tight_p_conv = False (converge density to 0.05xSqrt[SCFCRT]) scfconv = 0.100E-07 itrmax = 1000 printcharges = False peptide_corr = False qmqmrij_incore = False qmmmrij_incore = False qmqm_erep_incore = False pseudo_diag = False qm_ewald = 0 qm_pme = False | 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 QMMM: Warning: No Convergence in SCF Calculation; QMMM: Maximum Iteraction Count Has Been Reached QMMM: Job will continue with unconverged SCF QMMM: Energies and forces this step will not be accurate NSTEP ENERGY RMS GMAX NAME NUMBER 1 3.2061E+04 2.8410E+02 4.2371E+03 SG 373 BOND = 53.1269 ANGLE = 71.9091 DIHED = 175.6588 VDWAALS = 2120.6331 EEL = -3258.6199 EGB = 0.0000 1-4 VDW = 179.4333 1-4 EEL = 2324.2647 RESTRAINT = 0.0000 PM3ESCF = 30394.0977 QMMM: Warning: No Convergence in SCF Calculation; QMMM: Maximum Iteraction Count Has Been Reached QMMM: Job will continue with unconverged SCF QMMM: Energies and forces this step will not be accurate NSTEP ENERGY RMS GMAX NAME NUMBER 2 2.6934E+04 2.8497E+02 4.1406E+03 SG 373 BOND = 53.0511 ANGLE = 71.8919 DIHED = 175.6547 VDWAALS = 2067.0594 EEL = -3261.6987 EGB = 0.0000 1-4 VDW = 179.4359 1-4 EEL = 2324.2640 RESTRAINT = 0.0000 PM3ESCF = 25324.7424 QMMM: Warning: No Convergence in SCF Calculation; QMMM: Maximum Iteraction Count Has Been Reached QMMM: Job will continue with unconverged SCF QMMM: Energies and forces this step will not be accurate NSTEP ENERGY RMS GMAX NAME NUMBER 3 4.2558E+04 2.7869E+02 4.0233E+03 SG 373 BOND = 52.9662 ANGLE = 71.8746 DIHED = 175.6487 VDWAALS = 2006.1544 EEL = -3263.7008 EGB = 0.0000 1-4 VDW = 179.4385 1-4 EEL = 2324.2647 RESTRAINT = 0.0000 PM3ESCF = 41011.7709 QMMM: Warning: No Convergence in SCF Calculation; QMMM: Maximum Iteraction Count Has Been Reached QMMM: Job will continue with unconverged SCF QMMM: Energies and forces this step will not be accurate NSTEP ENERGY RMS GMAX NAME NUMBER 4 3.4399E+04 2.6814E+02 3.9609E+03 SG 373 BOND = 52.9241 ANGLE = 71.8658 DIHED = 175.6456 VDWAALS = 1976.5284 EEL = -3263.7096 EGB = 0.0000 1-4 VDW = 179.4391 1-4 EEL = 2324.2651 RESTRAINT = 0.0000 PM3ESCF = 32882.4373 QMMM: Warning: No Convergence in SCF Calculation; QMMM: Maximum Iteraction Count Has Been Reached QMMM: Job will continue with unconverged SCF QMMM: Energies and forces this step will not be accurate NSTEP ENERGY RMS GMAX NAME NUMBER 5 2.5444E+04 2.6066E+02 3.8853E+03 SG 373 BOND = 52.8720 ANGLE = 71.8569 DIHED = 175.6420 VDWAALS = 1940.6721 EEL = -3263.7199 EGB = 0.0000 1-4 VDW = 179.4404 1-4 EEL = 2324.2651 RESTRAINT = 0.0000 PM3ESCF = 23962.7079 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 5 2.5444E+04 2.6066E+02 3.8853E+03 SG 373 BOND = 52.8720 ANGLE = 71.8569 DIHED = 175.6420 VDWAALS = 1940.6721 EEL = -3263.7199 EGB = 0.0000 1-4 VDW = 179.4404 1-4 EEL = 2324.2651 RESTRAINT = 0.0000 PM3ESCF = 23962.7079 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb off-diag 0.03 (97.74% of Gen B) | Other 0.00 ( 2.26% of Gen B) | Gen Born time 0.03 (100.0% of Nonbo) | IPS excludes 0.00 ( 0.02% of Nonbo) | Nonbond force 0.03 ( 0.02% of Force) | QMMM 126.22 (100.0% of Force) | Force time 126.26 (100.0% of Runmd) | Runmd Time 126.26 (100.0% of Total) | Other 0.04 ( 0.04% of Total) | Total time 126.31 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 10:41:32.990 on 09/14/2006 | Setup done at 10:41:33.018 on 09/14/2006 | Run done at 10:43:39.296 on 09/14/2006 | wallclock() was called 133 times