------------------------------------------------------- Amber 12 SANDER 2012 ------------------------------------------------------- | Run on 06/11/2014 at 17:38:38 [-O]verwriting output File Assignments: | MDIN: _MMPBSA_gb_qmmm_rec.mdin | MDOUT: _MMPBSA_receptor_gb.mdout.0 |INPCRD: _MMPBSA_dummyreceptor.inpcrd | PARM: protein.prmtop |RESTRT: _MMPBSA_restrt.0 | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: _MMPBSA_receptor.mdcrd.0 | Here is the input file: File generated by MMPBSA.py &cntrl nsnb=99999, dec_verbose=0, ntb=0, surften=0.0072, ifqnt=1, extdiel=80.0, ncyc=0, cut=999.0, saltcon=0.1, imin=5, igb=5, / &qmmm qmmask=':123', qm_theory='PM3', qmcut=9999.0, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 06/05/14 Time = 14:21:07 NATOM = 6793 NTYPES = 14 NBONH = 3350 MBONA = 3520 NTHETH = 7598 MTHETA = 4772 NPHIH = 15063 MPHIA = 11822 NHPARM = 0 NPARM = 0 NNB = 37456 NRES = 431 NBONA = 3520 NTHETA = 4772 NPHIA = 11822 NUMBND = 42 NUMANG = 94 NPTRA = 43 NATYP = 28 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 469443 | Hollerith 20812 | Integer 382160 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 5241 kbytes | Note: 1-4 EEL scale factors are being read from the topology file. | Note: 1-4 VDW scale factors are being read from the topology file. | Duplicated 0 dihedrals | Duplicated 0 dihedrals LOADING THE QUANTUM ATOMS AS GROUPS Mask :123; matches 10 atoms -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- default_name General flags: imin = 5, 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 = 99999 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.10000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85000, surften = 0.00720 rdt = 0.00000, rgbmax = 25.00000 extdiel = 80.00000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 1, ncyc = 0, ntmin = 1 dx0 = 0.01000, drms = 0.00010 QMMM options: ifqnt = True nquant = 10 qmgb = 2 qmcharge = 0 adjust_q = 2 spin = 1 qmcut = ******** qmshake = 1 qmmm_int = 1 lnk_atomic_no = 1 lnk_dis = 1.0900 lnk_method = 1 qm_theory = PM3 verbosity = 0 qmqmdx = Analytical tight_p_conv = False (converge density to 0.05xSqrt[SCFCRT]) scfconv = 0.100E-07 itrmax = 1000 printcharges = False printdipole = False peptide_corr = False qmmmrij_incore = True qmqm_erep_incore = True pseudo_diag = True pseudo_diag_criteria = 0.0500 diag_routine = 1 qm_ewald = 0 qm_pme = False | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- Cpptraj Generated Restart begin time read from input coords = 1.000 ps Number of triangulated 3-point waters found: 0 QMMM: ADJUSTING CHARGES QMMM: ---------------------------------------------------------------------- QMMM: adjust_q = 2 QMMM: Uniformly adjusting the charge of MM atoms to conserve total charge. QMMM: qm_charge = 0 QMMM: QM atom RESP charge sum (inc MM link) = -0.818 QMMM: Adjusting each MM atom resp charge by = -0.000 QMMM: Sum of MM + QM region is now = -10.000 QMMM: ---------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES Cpptraj Generated trajectory minimizing coord set # 1 QMMM: Link Atom Information QMMM: ------------------------------------------------------------------------ QMMM: nlink = 2 Link Coords Resp Charges QMMM: MM(typ) - QM(typ) X Y Z MM QM QMMM: 1928 C 1930 N 41.595 55.138 37.013 0.597 -0.416 QMMM: 1940 N 1938 C 39.028 55.526 38.668 -0.416 0.597 QMMM: ------------------------------------------------------------------------ QMMM: QM Region Cartesian Coordinates (*=link atom) QMMM: QM_NO. MM_NO. ATOM X Y Z QMMM: 1 1930 N 41.5140 54.4420 37.8480 QMMM: 2 1931 H 42.3330 54.3310 38.4280 QMMM: 3 1932 C 40.2890 53.7060 38.2250 QMMM: 4 1933 H 40.1830 52.9390 37.4590 QMMM: 5 1934 C 40.6070 52.9250 39.5070 QMMM: 6 1935 H 41.4730 52.3400 39.1970 QMMM: 7 1936 H 39.8380 52.1530 39.5380 QMMM: 8 1937 S 40.8500 53.9820 41.0250 QMMM: 9 1938 C 39.0430 54.5060 38.2840 QMMM: 10 1939 O 38.0060 54.0030 37.8940 QMMM: 11 *H 41.5949 55.1378 37.0129 QMMM: 12 *H 39.0275 55.5260 38.6680 -------------------------------------------------------------------------------- 3.1 QM CALCULATION INFO -------------------------------------------------------------------------------- QMMM: System specified with odd number of electrons ( 35) QMMM: but odd spin ( 1). You most likely have the charge of QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.