------------------------------------------------------- Amber 16 SANDER 2016 ------------------------------------------------------- | Run on 04/28/2017 at 12:25:02 | Executable path: /opt/amber/bin/sander | Working directory: /home/budhdipe/gaussian_basis_trial | Hostname: comet-16-07 [-O]verwriting output File Assignments: | MDIN: amber_gauss_min.in | MDOUT: amber_gauss_testing_min.out |INPCRD: FABI_NDP_TCLC.inpcrd | PARM: FABI_NDP_TCL.prmtop |RESTRT: amber_gauss_min.rst | REFC: refc | MDVEL: mdvel | MDFRC: mdfrc | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj Here is the input file: #Initial minimization of our structure &cntrl imin=1 maxcyc=1000 ncyc=500 cut=10.0 ntb=1 ntc=2 ntf=2 ifqnt=1 &end &qmmm qmmask=':93,258' qmcharge=0 qm_theory='EXTERN' qm_ewald=0 &end &gau method='M062X' basis='6-311++G*' &end -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: 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 = 42.617 | New format PARM file being parsed. | Version = 1.000 Date = 02/27/17 Time = 14:41:02 NATOM = 51660 NTYPES = 21 NBONH = 49681 MBONA = 2011 NTHETH = 4467 MTHETA = 2723 NPHIH = 8840 MPHIA = 8585 NHPARM = 0 NPARM = 0 NNB = 85288 NRES = 16167 NBONA = 2011 NTHETA = 2723 NPHIA = 8585 NUMBND = 100 NUMANG = 214 NPTRA = 215 NATYP = 58 NPHB = 1 IFBOX = 1 NMXRS = 70 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 4117177 | Hollerith 171149 | Integer 2031093 | Max Pairs 29756160 | nblistReal 619920 | nblist Int 2049265 | Total 169851 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 :93,258; matches 34 atoms BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- default_name General flags: imin = 1, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 2, ntpr = 50, ntrx = 1, ntwr = 1 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 1, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 10.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 1000, ncyc = 500, ntmin = 1 dx0 = 0.01000, drms = 0.00010 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 0 Box X = 85.235 Box Y = 85.784 Box Z = 85.819 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 90 NFFT2 = 90 NFFT3 = 90 Cutoff= 10.000 Tol =0.100E-04 Ewald Coefficient = 0.27511 Interpolation order = 4 QMMM options: ifqnt = True nquant = 34 qmgb = 0 qmcharge = 0 adjust_q = 2 spin = 1 qmcut = 10.0000 qmshake = 1 qmmm_int = 1 lnk_atomic_no = 1 lnk_dis = 1.0900 lnk_method = 1 qm_theory = EXTERN verbosity = 0 qmqmdx = Analytical qm_ewald = 0 qm_pme = False -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- default_name begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 15905 Sum of charges from parm topology file = -0.00010217 Forcing neutrality... 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) = 0.343 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 = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 15768742 | TOTAL SIZE OF NONBOND LIST = 15768742 QMMM: Link Atom Information QMMM: ------------------------------------------------------------------------ QMMM: nlink = 2 Link Coords Resp Charges QMMM: MM(typ) - QM(typ) X Y Z MM QM QMMM: 1428 C 1430 N -4.738 2.205 -0.959 0.597 -0.416 QMMM: 1440 N 1438 C -7.612 -0.642 0.179 -0.255 0.597 QMMM: ------------------------------------------------------------------------ QMMM: QM Region Cartesian Coordinates (*=link atom) QMMM: QM_NO. MM_NO. ATOM X Y Z QMMM: 1 1430 N -4.9757 1.2629 -0.4658 QMMM: 2 1431 H -4.4897 1.0171 0.3848 QMMM: 3 1432 C -5.9750 0.3403 -0.9800 QMMM: 4 1433 H -6.7917 0.8324 -1.5081 QMMM: 5 1434 C -5.3410 -0.7018 -1.9171 QMMM: 6 1435 H -4.5273 -1.2095 -1.3993 QMMM: 7 1436 H -6.0946 -1.4319 -2.2124 QMMM: 8 1437 H -4.9512 -0.2035 -2.8048 QMMM: 9 1438 C -6.5665 -0.3383 0.2401 QMMM: 10 1439 O -5.8643 -0.5196 1.2452 QMMM: 11 3918 C 5.1182 -1.5401 -0.8658 QMMM: 12 3919 C 5.7245 -2.2048 0.2482 QMMM: 13 3920 C 4.2122 -0.4536 -0.6396 QMMM: 14 3921 C 3.9206 -0.0391 0.6729 QMMM: 15 3922 C 4.5220 -0.6978 1.7944 QMMM: 16 3923 C 5.4226 -1.7834 1.5692 QMMM: 17 3924 C -1.0693 0.3272 1.5921 QMMM: 18 3925 C -0.5570 1.6729 1.6911 QMMM: 19 3926 C 0.8216 1.8875 1.4404 QMMM: 20 3927 C 1.6763 0.7690 1.0964 QMMM: 21 3928 C -0.2385 -0.7728 1.2558 QMMM: 22 3929 C 1.1337 -0.5646 1.0059 QMMM: 23 3930 O 3.0285 1.0304 0.8600 QMMM: 24 3931 Cl 6.7917 -3.4845 0.0028 QMMM: 25 3932 Cl -2.7039 0.0715 1.8906 QMMM: 26 3933 Cl 1.4398 3.4845 1.5568 QMMM: 27 3934 O 3.6084 0.2095 -1.6694 QMMM: 28 3935 H -0.6602 -1.7726 1.1910 QMMM: 29 3936 H 5.3457 -1.8604 -1.8793 QMMM: 30 3937 H 4.2911 -0.3701 2.8048 QMMM: 31 3938 H 5.8778 -2.2879 2.4176 QMMM: 32 3939 H -1.2243 2.4902 1.9522 QMMM: 33 3940 H 1.7813 -1.3982 0.7466 QMMM: 34 3941 H 3.0340 0.9102 -1.3120 QMMM: 35 *H -4.7377 2.2055 -0.9588 QMMM: 36 *H -7.6115 -0.6418 0.1788 -------------------------------------------------------------------------------- 3.1 QM CALCULATION INFO -------------------------------------------------------------------------------- | Please also cite the following work for the use of the QM/MM interface: | A. W. G"otz, M. A. Clark, R. C. Walker | "An extensible interface for ab initio QM/MM molecular dynamics simulations | with AMBER" | J. Comput. Chem. 35 (2014) 95-108. | DOI: 10.1002/jcc.23444 Constants for unit conversion taken from Mohr, Taylor, Newell, Rev. Mod. Phys. 80 (2008) 633-730 and using the thermochemical calorie (1 cal = 4.184 J): A_TO_BOHRS = 1.889726132873E+00 AU_TO_KCAL = 6.2750946943E+02 AU_TO_DEBYE = 2.54174623E+00 >>> Running calculations with Gaussian <<< | &gau | method = M062X | basis = 6-311++G* | guess = read | mem = 256MB | scf_conv = 8 | ntpr = 50 | num_threads = 1 | debug = 0 | dipole = F | use_template = F | / | Program g09 found! | Executable location: /opt/gaussian/09.D.01/g09/g09 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- SANDER BOMB in subroutine get_gau_forces (qm2_extern_gau_module) Error with system call (executing Gaussian) Will quit now.