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From: Huang Jing <jing.huang8911.gmail.com>

Date: Thu, 12 Jan 2017 00:33:17 +0200

The tutorial:

http://nf.nci.org.au/~vvv900/monash/amber-gaussian/index.html

jing

On Wed, Jan 11, 2017 at 11:55 PM, Aseel Bala <balaahme.msu.edu> wrote:

*> Hi everyone,
*

*>
*

*>
*

*>
*

*> I am using the sander interface to run a QM calculation on one molecule
*

*> (Butanol- 15 atoms) in a box. I am including other molecules whose have
*

*> atoms that fall within a certain distance around the QM molecule as point
*

*> charges.
*

*>
*

*>
*

*>
*

*> My input to sander (qm.in) looks as follows:
*

*>
*

*> Testing tutorial on website for QMMM with Gaussian
*

*>
*

*> &cntrl
*

*>
*

*> imin=0,nstlim = 0, !do not run a minimization or MD run
*

*>
*

*> ntb=2, !constant pressure periodic boundary conditions
*

*>
*

*> ntf=2,ntc=2,
*

*>
*

*> cut=10.0, !10 ang classic bond cutoff
*

*>
*

*> ntp=1,
*

*>
*

*> ifqnt=1 !switch on QM/MM
*

*>
*

*> &end
*

*>
*

*> &qmmm
*

*>
*

*> qmmask='.16-30',
*

*>
*

*> qmcharge=0,
*

*>
*

*> qm_theory='EXTERN',
*

*>
*

*> qmcut=10.0,
*

*>
*

*> qm_ewald = 0 !Use a real-space cutoff for QM-QM and QM-MM long range
*

*> interactions.
*

*>
*

*> &end
*

*>
*

*> &gau
*

*>
*

*> method = 'B3LYP',
*

*>
*

*> basis = '6-31G* Freq',
*

*>
*

*> &end
*

*>
*

*>
*

*>
*

*> Atoms 16-30 here belong to the molecule that I want to calculate quantum
*

*> mechanically. Then I run the command:
*

*>
*

*>
*

*>
*

*> sander -O -i qm2.in -o qm2.out -c ../../c2.inpcrd -p
*

*> ../../../simbox.prmtop
*

*>
*

*>
*

*>
*

*> I get several outputs including the file that sander used as an input to
*

*> Gaussian which I attached here (old.gau.job.inp). The beginning of the file
*

*> looks like this:
*

*>
*

*> %chk=gau_job.chk
*

*>
*

*> %NProcShared=1
*

*>
*

*> %mem=256MB
*

*>
*

*> #P B3LYP/6-31G* Freq SCF=(Conver=8) NoSymm Charge Prop=(Field,Read)
*

*>
*

*>
*

*>
*

*> Gaussian run using SANDER external interface.
*

*>
*

*>
*

*>
*

*> 0 1
*

*>
*

*> C 1.7629999999999992 -0.6445000000000007
*

*> 0.6690000000000013
*

*>
*

*> C 0.5479999999999994 -0.8485000000000007
*

*> -0.2869999999999987
*

*>
*

*> C -0.4740000000000007 0.2914999999999993
*

*> -0.3389999999999986
*

*>
*

*> C -1.8300000000000007 -0.0425000000000007
*

*> -0.8029999999999987
*

*>
*

*> O -2.5260000000000002 1.1444999999999992
*

*> -1.0729999999999986
*

*>
*

*> H -1.9130000000000005 1.7184999999999993
*

*> -1.5379999999999985
*

*>
*

*> H 2.5259999999999994 -1.3325000000000007
*

*> 0.3040000000000012
*

*>
*

*> H 1.5289999999999992 -0.9005000000000007
*

*> 1.7020000000000013
*

*>
*

*> H 2.1819999999999995 0.3554999999999993
*

*> 0.5600000000000012
*

*>
*

*> H 0.0029999999999993 -1.7185000000000008
*

*> 0.0770000000000013
*

*>
*

*> H 0.8539999999999993 -1.0945000000000007
*

*> -1.3039999999999985
*

*>
*

*> H -0.5540000000000007 0.6844999999999992
*

*> 0.6740000000000012
*

*>
*

*> H -0.0540000000000007 1.0024999999999995
*

*> -1.0509999999999988
*

*>
*

*> H -1.6770000000000007 -0.6405000000000007
*

*> -1.7019999999999984
*

*>
*

*> H -2.3290000000000006 -0.6755000000000007
*

*> -0.0689999999999987
*

*>
*

*>
*

*>
*

*> 11.6699999999999999 1.8194999999999990 2.9420000000000011
*

*> 0.0914000055333610
*

*>
*

*> 10.7509999999999994 1.7334999999999996 1.8860000000000012
*

*> -0.5467999944666389
*

*>
*

*> 9.9049999999999994 1.5534999999999992 2.3030000000000013
*

*> 0.4050000055333611
*

*>
*

*> 11.4599999999999991 2.8114999999999992 3.3430000000000013
*

*> 0.0112000055333610
*

*>
*

*> 11.5770000000000000 1.0224999999999993 3.6800000000000010
*

*> 0.0112000055333610
*

*>
*

*> 7.9059999999999988 -3.2045000000000008 1.3910000000000013
*

*> -0.1850999944666389
*

*>
*

*> 8.1440000000000001 -2.2615000000000007 2.5240000000000009
*

*> 0.0026000055333610
*

*>
*

*> 7.8429999999999991 -0.7435000000000007 2.2410000000000014
*

*> -0.2023999944666389
*

*>
*

*> ...
*

*>
*

*>
*

*>
*

*> >From what I saw online, this file starts off with a symbolic Z matrix
*

*> which
*

*> should state the Cartesian coordinates of the atoms in the QM region (top
*

*> set of lines) and then the coordinates (and charge) of all the atoms
*

*> considered as point charges (second set of lines).
*

*>
*

*>
*

*>
*

*> The issue is that there seems to be a manipulation of the coordinates
*

*> before
*

*> this file is formed because these numbers do not match with the coordinates
*

*> in the inpcrd I give sander for neither the QM atoms or the point charges.
*

*> I
*

*> also don't know how the charges are being calculated in this file since
*

*> they
*

*> also don't match the prmtop file I included in the input.
*

*>
*

*>
*

*>
*

*> Does anyone know how the input to Gaussian is generated by sander? I am
*

*> attaching all my files in this email in case they might help.
*

*>
*

*> I would really appreciate any insight into this.
*

*>
*

*>
*

*>
*

*> Thanks everyone,
*

*>
*

*> --
*

*>
*

*>
*

*>
*

*> Aseel Bala Ahmed
*

*>
*

*> PhD Candidate, Chemical Engineering
*

*>
*

*> Michigan State University
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

*>
*

Date: Thu, 12 Jan 2017 00:33:17 +0200

The tutorial:

http://nf.nci.org.au/~vvv900/monash/amber-gaussian/index.html

jing

On Wed, Jan 11, 2017 at 11:55 PM, Aseel Bala <balaahme.msu.edu> wrote:

-- ---------------------- Dr. Jing Huang *Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum* *Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, Jerusalem 91904, Israel* _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Jan 11 2017 - 15:00:02 PST

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