AMBER Archive (2007)

Subject: Re: AMBER: antechamber for topology file

From: FyD (fyd_at_u-picardie.fr)
Date: Wed Feb 07 2007 - 07:28:58 CST

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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