Re: AMBER: antechamber for topology file

From: FyD <>
Date: Wed, 07 Feb 2007 14:28:58 +0100

Quoting deepti nayar <>:

> 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.
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 - 06:07:05 PST
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