Re: [AMBER] Starting antechamber for preparing ligand molecule

From: FyD <>
Date: Wed, 18 Mar 2015 14:09:04 +0100

Dear Anasuya,

R.E.D. Server/Ante_RED & RED IV are outdated!
Please switch to R.E.D. Server Dev./PyRED .:

Click on the "Mini How-To" link, that is supposed to summarize all the
available pieces of information... ouf...

regards, Francois

>> 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 - 06:30:03 PDT
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