Re: [AMBER] Sander input into Gaussian

From: Aseel Bala <balaahme.msu.edu> Date: Thu, 12 Jan 2017 13:17:37 -0500

--
Aseel Bala Ahmed
PhD Candidate, Chemical Engineering
Michigan State University
-----Original Message-----
From: Huang Jing [mailto:jing.huang8911.gmail.com] 
Sent: Wednesday, January 11, 2017 5:33 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Sander input into Gaussian
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
>
>
>
>
>
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
----------------------
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*
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