AMBER Archive (2006)

Subject: RE: AMBER: parameters for Nickel and iron

From: Junmei Wang (jwang_at_encysive.com)
Date: Tue Sep 19 2006 - 11:16:26 CDT

I think you might first generate residue topologies (prep files) for
those non-standard amino acids. Please go to
http://amber.scripps.edu/antechamber/example.html to learn how to do
that.
 
All the best
 
Junmei
 
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,
        Rachel
        
         
        On 9/19/06, Fenghui Fan <fenghui_fan_at_yahoo.com> 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 <comeonsos_at_googlemail.com> 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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