AMBER Archive (2007)

Subject: Re: AMBER: antechamber for topology file

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Wed Feb 07 2007 - 06:32:52 CST

there are tutorials for things like this- have you worked
through them? Try a google search for
amber tutorial non-standard amino

deepti nayar wrote:

> hi
>
> 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.
>
>
> kindly help
>
>
> deepti
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