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.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.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
> >
>
>
> __________________________________________________
> Do You Yahoo!?
> Tired of spam? Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com
> ----------------------------------------------------------------------
> -
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
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.qtp.ufl.edu
http://www.qtp.ufl.edu/~merz
Phone: 352-392-6973
FAX: 352-392-8722
Cell: 814-360-0376
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Sep 20 2006 - 06:07:21 PDT
