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
