AMBER Archive (2006)

Subject: Re: AMBER: parameters for Nickel and iron

From: Rachel (comeonsos_at_googlemail.com)
Date: Thu Sep 21 2006 - 06:50:23 CDT

Hi, all,

Thanks very much for all your replies, which are quite helpful :)

However, Junmei, after I read the information you gave about using
antechamber I still don't quite understand how to use it. For example, I
have Ni ions bound to four CYS residues (e.g. CYS11, CYS35, CYS100, CYS218),
do I just need to cut these residues from the original PDB file and follow
the procedures? Do I need to have Gaussian software or it can be done only
using antechamber? And also the way it tells is quite different from what
the amber workshop tutorial 5 does it, can you please tell me more about it?
I tried to cut those residues out from the PDB and followed the tutorial 5,
it gave me error message 'can't open ANTECHAMBER_AM1BCC.AC', why is that?
Thanks a lot, I am such a newbie in this, and thank you very much in
advance.

Best regards,
Rachel

On 9/19/06, Ken Merz <merz_at_qtp.ufl.edu> wrote:
>
> 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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