Re: AMBER: antechamber for topology file

From: deepti nayar <deepti.icgeb.gmail.com>
Date: Thu, 8 Feb 2007 12:25:35 +0530

thanx for d help akshay



can u tell me d link/site from where to get ths gaussian program.


On 2/8/07, Akshay Patny <akshay17.olemiss.edu> wrote:
> Hi Deepti
>
> I doubt if you can run gaussian job within amber. The gaussian input
> file you have got from antechamber can be submitted to gaussian
> program to get the output file.
>
> Here is how I did for my system >>>
>
> ------------------------------------------------------------------------------------------------------------------
> I generated the gaussian input file using antechamber, as
> follows:
>
> % antechamber fi mol2 i DMPC_mono_sybyl.mol2 fo
> gcrt o DMPC_mono.com
>
> Then, using the generated input file, I ran a gaussian job,
> as follows:
>
> % g03sub n 1 DMPC_mono.com
>
> Then I used the gaussian output in antechamber to do the
> 2-stage RESP fitting as follows:
>
> % antechamber -rn DMP -fi gout -i H1DMPC_mono.out -fo prepi
> -o DMPC_mono_resp.prep -c resp -s 2
>
> This gave me the prep file, which I checked using PARMCHK
> utility, as follows:
>
> % parmchk -i DMPC_mono_resp.prep -f prepi -o
> DMPC_mono_frcmod
>
> ------------------------------------------------------------------------------------------------------------------
>
> Hope this helps. Please correct if I am wrong.
>
> Best, -Akshay
>
> = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
> Akshay Patny
> PhD Candidate (5th Yr.), Computational Chemistry
> Department of Medicinal Chemistry, School of Pharmacy
> The University of Mississippi
> 805 College Hill Rd, # 9, Oxford, MS 38655
> E-mail: akshay17.olemiss.edu
> Phone (O): (662)-915-1286,(M): (662)-801-5496
> = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
>
> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On
> Behalf Of deepti nayar
> Sent: Thursday, February 08, 2007 12:07 AM
> To: amber.scripps.edu
> Subject: Re: AMBER: antechamber for topology file
>
> thank u so much for the help. im using antechamber now to generate
> topology file. i wanted to know how to run gaussian in amber?? what is
> the command? i have a gaussian input file which i got after running in
> antehamber. nw i want gaussian output file and for that purpose i have
> to use gaussian. bt i dont know how??
>
> plz help
>
> On 2/7/07, FyD <fyd.u-picardie.fr> wrote:
> > Quoting deepti nayar <deepti.icgeb.gmail.com>:
> >
> > > i have to simulate a peptide containing a non standard residue. ito be
> > > more precise, i have to simulate a dipeptide containing dehydroamino
> > > acid residue. i have to simulate a peptide containing a
> > > dehydrophenylalanine and dehydro del phenylalanine residue. so if i
> > > load the standard force field ff99. how should i make a topology file
> > > for ths non standard residue. i guess i have to use antechamber as
> > > some of u told me. what all is required for making a topology file in
> > > antechamber.
> >
> > You can also use R.E.D. that generates Tripos mol2 files with charge
> > values and topology information.
> >
> > You have many examples of non-standard aminoacids in R.E.DD.B.
> > http://www.u-picardie.fr/labo/lbpd/REDDB/
> > Just use the "List projects" R.E.DD.B. tool, select "Molecule
> > fragment" & click on "Display".
> >
> > regards, Francois
> >
> >
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Received on Sun Feb 11 2007 - 06:07:17 PST
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