AMBER Archive (2007)

Subject: Re: AMBER: antechamber for topology file

From: deepti nayar (deepti.icgeb_at_gmail.com)
Date: Thu Feb 08 2007 - 00:07:22 CST

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
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu