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[求助]
gaussian-amber 联用问题
按照gaussian-amber 联用教程进行模拟计算,教程如下,前面都很顺利,最后一步计算也输出了文件,但是很快就输出了,最后看了一下输出文件amber-g09-min.out,发现gaussian软件没有启动,不知道什么原因,gaussian单独计算可以顺利完成,但是在sander下就计算不了,不知道为什么gaussian启动不了?
$ 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(这一步出了问题)
amber-g09-min.out文件内容如下:
-------------------------------------------------------
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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