Re: [AMBER] Starting antechamber for preparing ligand molecule

From: Hannes Loeffler <>
Date: Wed, 18 Mar 2015 09:15:38 +0000

On Tue, 17 Mar 2015 22:53:51 +0530
Anasuya Dighe <> wrote:

> Dear Amber Users,
> I am interested in starting the simulation on a protein ligand
> complex.
> The ligand in question is a peptide inhibitor called Pepstatin. This
> molecule has the Isovaleric Acid (IVA) and Statin (STA) chemical
> moieties. These chemical moieties are connected to each other by a
> series of amino acids, namely VAL (Valine) and ALA (Alanine). I have
> the following questions.

I think it is generally not recommended to use GAFF and AM1/BCC charges
for standard residues but rather use the parameters from the standard
protein force field. This leaves you, as far as a I can see, with
three non-standard residues: IVA, STA in mid-position and STA in
terminal position. The best approach would probably be a residue based
approach as has been used in obtaining parameters for the standard
force field (see the relevant papers which probably have been cited in
the manual). I understand that the R.E.D. server and associated tools
can be quite helpful in doing this. A literature search may turn up
useful results too.


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Received on Wed Mar 18 2015 - 02:30:04 PDT
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