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xzhfood榮譽(yù)版主 (著名寫手)
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gaussian-amber 聯(lián)用問題
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按照gaussian-amber 聯(lián)用教程進(jìn)行模擬計(jì)算，教程如下，前面都很順利，最后一步計(jì)算也輸出了文件，但是很快就輸出了，最后看了一下輸出文件amber-g09-min.out，發(fā)現(xiàn)gaussian軟件沒有啟動(dòng)，不知道什么原因，gaussian單獨(dú)計(jì)算可以順利完成，但是在sander下就計(jì)算不了，不知道為什么gaussian啟動(dòng)不了？ $ tleap -s -f leaprc.ff12SB -I: Adding /apps/amber/12/dat/leap/prep to search path. -I: Adding /apps/amber/12/dat/leap/lib to search path. -I: Adding /apps/amber/12/dat/leap/parm to search path. -I: Adding /apps/amber/12/dat/leap/cmd to search path. -s: Ignoring startup file: leaprc -f: Source leaprc.ff12SB. Welcome to LEaP! Sourcing: /apps/amber/12/dat/leap/cmd/leaprc.ff12SB Log file: ./leap.log Loading parameters: /apps/amber/12/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA Loading parameters: /apps/amber/12/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters Loading library: /apps/amber/12/dat/leap/lib/amino12.lib Loading library: /apps/amber/12/dat/leap/lib/aminoct12.lib Loading library: /apps/amber/12/dat/leap/lib/aminont12.lib Loading library: /apps/amber/12/dat/leap/lib/nucleic12.lib Loading library: /apps/amber/12/dat/leap/lib/ions08.lib Loading library: /apps/amber/12/dat/leap/lib/solvents.lib Create histidine aminoacid: > his=sequence {ACE HIS NME} > desc his UNIT name: ACE Head atom: null Tail atom: null Contents: R<ACE 1> R<HIE 2> R<NME 3> Now save the 3d structure in PDB format (for visualization) > savepdb his his-ini.pdb Writing pdb file: his-ini.pdb Also save molecular topology and 3d coordinates for sander. > saveamberparm his his.top his.crd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 8 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (no restraints) > quit Quit sander -O -i amber-g09-min.in -o amber-g09-min.out -c his.crd -p his.top -r amber-g09-min.rst（這一步出了問題） amber-g09-min.out文件內(nèi)容如下： ------------------------------------------------------- Amber 12 SANDER 2012 ------------------------------------------------------- | Run on 04/15/2019 at 06:05:04 [-O]verwriting output File Assignments: | MDIN: amber-g09-min.in | MDOUT: amber-g09-min.out |INPCRD: his.crd | PARM: his.top |RESTRT: amber-g09-min.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj | Here is the input file: Example QM/MM input for Sander-12 - Gaussian interface &cntrl imin=1, maxcyc=10, ntb=0, cut=20., ifqnt=1 &end &qmmm qmmask='@11-21', qmcharge=0, qm_theory='EXTERN', qmcut=20.0 &end &gau method = BLYP, basis = 6-31G, charge = 0, &end -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation | *** cutoff > system size, list only builds once |Largest sphere to fit in unit cell has radius = 31.897 | New format PARM file being parsed. | Version = 1.000 Date = 04/15/19 Time = 03:13:44 NATOM = 29 NTYPES = 9 NBONH = 14 MBONA = 15 NTHETH = 30 MTHETA = 19 NPHIH = 57 MPHIA = 48 NHPARM = 0 NPARM = 0 NNB = 138 NRES = 3 NBONA = 15 NTHETA = 19 NPHIA = 48 NUMBND = 20 NUMANG = 36 NPTRA = 42 NATYP = 15 NPHB = 0 IFBOX = 0 NMXRS = 17 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 3136 | Hollerith 92 | Integer 25827 | Max Pairs 406 | nblistReal 348 | nblist Int 86723 | Total 468 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 @11-21; matches 11 atoms -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- ACE 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 = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 20.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 10, ncyc = 10, ntmin = 1 dx0 = 0.01000, drms = 0.00010 QMMM options: ifqnt = True nquant = 11 qmgb = 0 qmcharge = 0 adjust_q = 2 spin = 1 qmcut = 20.0000 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 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- ACE begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 Sum of charges from parm topology file = -0.00000000 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) = -0.022 QMMM: Adjusting each MM atom resp charge by = -0.001 QMMM: Sum of MM + QM region is now = 0.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- eedmeth=4: Setting switch to one everywhere --------------------------------------------------- | Local SIZE OF NONBOND LIST = 257 | TOTAL SIZE OF NONBOND LIST = 257 QMMM: Link Atom Information QMMM: ------------------------------------------------------------------------ QMMM: nlink = 1 Link Coords Resp Charges QMMM: MM(typ) - QM(typ) X Y Z MM QM QMMM: 9 CX 11 CT 5.084 4.502 -0.351 -0.058 -0.007 QMMM: ------------------------------------------------------------------------ QMMM: QM Region Cartesian Coordinates (*=link atom) QMMM: QM_NO. MM_NO. ATOM X Y Z QMMM: 1 11 C 5.6613 4.2208 -1.2321 QMMM: 2 12 H 5.8085 3.1409 -1.2414 QMMM: 3 13 H 5.1233 4.5214 -2.1312 QMMM: 4 14 C 7.0335 4.8447 -1.3211 QMMM: 5 15 N 7.8926 4.5867 -2.3830 QMMM: 6 16 C 9.0051 5.2681 -2.1825 QMMM: 7 17 H 9.8193 5.2069 -2.9046 QMMM: 8 18 N 8.8989 5.9379 -1.0617 QMMM: 9 19 H 9.6126 6.5402 -0.6769 QMMM: 10 20 C 7.6863 5.7028 -0.4925 QMMM: 11 21 H 7.4253 6.1816 0.4513 QMMM: 12 *H 5.0838 4.5018 -0.3515 -------------------------------------------------------------------------------- 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. 2013 | 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 <<< SANDER BOMB in subroutine get_namelist (qm2_extern_gau_module) The charge and spin keywords are deprecated Please specify charge (qmcharge) and spin multiplicity (spin) in the &qmmm namelist. 教程地址： http://sf.anu.edu.au/collaborati ... gaussian/index.html |
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