AMBER Archive (2007)

Subject: RE: AMBER: antechamber for topology file

From: Akshay Patny (akshay17_at_olemiss.edu)
Date: Thu Feb 08 2007 - 00:28:50 CST

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_at_olemiss.edu
Phone (O): (662)-915-1286,(M): (662)-801-5496
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = =

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On
Behalf Of deepti nayar
Sent: Thursday, February 08, 2007 12:07 AM
To: amber_at_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_at_u-picardie.fr> wrote:
> Quoting deepti nayar <deepti.icgeb_at_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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