------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 01/24/2007 at 19:52:35 [-O]verwriting output File Assignments: | MDIN: min1.in | MDOUT: min1.out |INPCRD: thermolysin.inpcrd | PARM: thermolysin.prmtop |RESTRT: min1.rst | REFC: thermolysin.inpcrd | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Thermolysin: initial minimisation solvent &cntrl imin = 1, maxcyc = 5000, ncyc = 2000, ntb = 1, ntr = 1, cut = 9, ifqnt =1 / &qmmm iqmatoms=2106,2107,2108,2109,2110,2111,2112,2113,2114,2115,2116,2171,2172,217 2336,2337,2338,2339,2340,2341,2342,2343,2344,2458,2459,2460,2461,246 4714,4715, qmtheory=1, qm_ewald=1,qm_pme=1 / Hold the Thermolysin fixed 500.0 RES 1 323 END END -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: MPI MMTSB getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read | peek_ewald_inpcrd: Box info found |Largest sphere to fit in unit cell has radius = 35.904 | New format PARM file being parsed. | Version = 1.000 Date = 01/24/07 Time = 13:38:38 NATOM = 37781 NTYPES = 18 NBONH = 35344 MBONA = 2491 NTHETH = 5105 MTHETA = 3393 NPHIH = 10186 MPHIA = 7744 NHPARM = 0 NPARM = 0 NNB = 69859 NRES = 11345 NBONA = 2491 NTHETA = 3393 NPHIA = 7744 NUMBND = 42 NUMANG = 89 NPTRA = 47 NATYP = 31 NPHB = 1 IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 2616446 | Hollerith 238033 | Integer 1184817 | Max Pairs 4190542 | nblistReal 453372 | nblist Int 1466518 | Total 51638 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 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 = 1, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 9.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 1 Energy minimization: maxcyc = 5000, ncyc = 2000, ntmin = 1 dx0 = 0.01000, drms = 0.00010 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 0 Box X = 88.588 Box Y = 71.808 Box Z = 73.748 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 90 NFFT2 = 72 NFFT3 = 75 Cutoff= 9.000 Tol =0.100E-04 Ewald Coefficient = 0.30768 Interpolation order = 4 QMMM options: ifqnt = True nquant = 58 qmgb = 0 qmcharge = 0 adjust_q = 2 spin = 1 qmcut = 9.0000 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 = True qmmmrij_incore = True qmqm_erep_incore = True pseudo_diag = True pseudo_diag_criteria = 0.0500 qm_ewald = 1 qm_pme = True kmaxqx = 5 kmaxqy = 5 kmaxqz = 5 ksqmaxq = 27 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES ----- READING GROUP 1; TITLE: Hold the Thermolysin fixed GROUP 1 HAS HARMONIC CONSTRAINTS 500.00000 GRP 1 RES 1 TO 323 Number of atoms in this group = 4715 ----- 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: 11022 | Atom division among processors: | 0 9446 18890 28337 37781 |QMMM: Running QMMM calculation in parallel mode on 4 threads. |QMMM: All atom division among threads: |QMMM: Start End Count |QMMM: Thread( 0): 1-> 9446 ( 9446) |QMMM: Thread( 1): 9447-> 18892 ( 9446) |QMMM: Thread( 2): 18893-> 28338 ( 9446) |QMMM: Thread( 3): 28339-> 37781 ( 9443) |QMMM: Quantum atom + link atom division among threads: |QMMM: Start End Count |QMMM: Thread( 0): 1-> 15 ( 15) |QMMM: Thread( 1): 16-> 30 ( 15) |QMMM: Thread( 2): 31-> 45 ( 15) |QMMM: Thread( 3): 46-> 63 ( 18) Sum of charges from parm topology file = -0.00000036 Forcing neutrality... | Running AMBER/MPI version on 4 nodes QMMM: ADJUSTING CHARGES QMMM: ---------------------------------------------------------------------- QMMM: adjust_q = 2 QMMM: Uniformally adjusting the charge of MM atoms to conserve total charge. QMMM: qm_charge = 0 QMMM: QM atom RESP charge sum (inc MM link) = 1.414 QMMM: Adjusting each MM atom resp charge by = 0.000 QMMM: Sum of MM + QM region is now = 0.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION using 5000.0 points per unit in tabled values TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff | CHECK switch(x): max rel err = 0.3338E-14 at 2.509280 | CHECK d/dx switch(x): max rel err = 0.8261E-11 at 2.768360 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 2335449 | TOTAL SIZE OF NONBOND LIST = 8648512 |QMMM: KVector division among threads: |QMMM: Start End Count |QMMM: Thread( 0): 1-> 78 ( 78) |QMMM: Thread( 1): 79-> 156 ( 78) |QMMM: Thread( 2): 157-> 234 ( 78) |QMMM: Thread( 3): 235-> 309 ( 75) QMMM: Link Atom Information QMMM: ------------------------------------------------------------------------ QMMM: nlink = 5 Link Coords Resp Charges QMMM: MM(typ) - QM(typ) X Y Z MM QM QMMM: 2104 CT 2106 CT -1.264 4.238 5.885 0.031 -0.152 QMMM: 2169 CT 2171 CT -4.084 4.324 -0.347 0.031 -0.152 QMMM: 2328 CT 2330 CT -0.066 -1.706 -7.088 0.010 -0.052 QMMM: 2456 CT 2458 CT 3.694 1.667 -0.533 0.032 0.075 QMMM: 2500 CT 2502 CT 1.071 5.338 2.416 0.118 0.147 QMMM: ------------------------------------------------------------------------ -------------------------------------------------------------------------------- 3.1 QM CALCULATION INFO --------------------------------------------------------------------------------