AMBER Archive (2006)

Subject: Re: AMBER: parameters for Nickel and iron

From: Ken Merz (merz_at_qtp.ufl.edu)
Date: Tue Sep 19 2006 - 15:00:51 CDT

Hi,
  We have done a bit on Ni, but in terms of your system it might not
help (see attached link). In general, you have to build your model
from scratch for a metallocluster. There are decent parameters
available for hemes, but for more complicated clusters it will take
some effort to build a model that works well. Good luck. Kennie

http://pubs.acs.org/cgi-bin/abstract.cgi/bichaw/2006/45/i14/abs/
bi052020p.html

On Sep 19, 2006, at 12:00 PM, Rachel wrote:

> 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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Professor Kenneth M. Merz, Jr.
Department of Chemistry
Quantum Theory Project
2328 New Physics Building
PO Box 118435
University of Florida
Gainesville, Florida 32611-8435

e-mail: merz_at_qtp.ufl.edu
http://www.qtp.ufl.edu/~merz

Phone: 352-392-6973
FAX: 352-392-8722
Cell: 814-360-0376

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