RE: AMBER: parameters for Nickel and iron

From: Junmei Wang <>
Date: Tue, 19 Sep 2006 11:16:26 -0500

I think you might first generate residue topologies (prep files) for
those non-standard amino acids. Please go to to learn how to do
All the best
Subject: Re: AMBER: parameters for Nickel and iron

        Hi, Fenghui,
        Thanks for your reply, I have tried Antechamber, however, as far
as i know, Antechamber is only suitable for small molecules, is it? And
the protein I want to study is pretty big with several thousands atoms
excluding hydrogen.
        I really appreciate it if anyone could tell me where can I find
such parameters.
        Best regards,
        On 9/19/06, Fenghui Fan <> wrote:

                I just want to discuss with you. Can you use
                Antechamber for this purpose? It is rather easy.
                I am looking forward to getting your reply on these
                especially to me.
                Best regards.
                Fenghui Fan
                --- Rachel <> wrote:
> Dear all AMBER users,
> The protein I wish to study contains nickel atom
> bonded with iron and CYS
> residues (by S), while the iron atom is bonded with
> CYS (by S) and HIS (by
> ND). I am trying to create the frcmod file for these
> non-standard metallic
> ions and its bonded residues, can anyone tell me
> where can i find the
> parameters for Fe and Ni please? Thanks a lot in
> advance!!
> With my best regards,
> Rachel

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Received on Wed Sep 20 2006 - 06:07:19 PDT
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