Hi Sel,
there are Zinc parameters for Amber using the cation dummy atom method
(CaDA). I'm using it right now and my first impression is that it works very
well.
http://mayoresearch.mayo.edu/mayo/research/camdl/zinc_protein.cfm
Cheers,
Oliver
2011/7/12 Ben Roberts <ben.roberts.geek.nz>
> Hi Sel,
>
> On 12/7/2011, at 1:00 p.m., Sel Ercan wrote:
>
> > hi all!
> > I have a protein which two CYS and two HIS coordinated with zinc. I need
> angle and torsion parameters.
> > Angle parameters:
> > <snip>
> >
> >
> > torsion parameters:
> > <snip>
>
> The most recent release of AmberTools, 1.5, contains MTK++, which includes
> programs for computing force-field terms for metal clusters in proteins.
> You
> could well find it useful for this purpose. Researchers in my group have
> used it
> to develop zinc/protein force fields.
>
> Regards,
> Ben
> --
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--
Oliver Kuhn, Department of Bioinformatics,
Center for Medical Biotechnology, University of Duisburg-Essen,
Universitätsstr. 1-5, 45141 Essen, Germany
phone +49 201 183-3121, oliver.kuhn.uni-due.de
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Received on Tue Jul 12 2011 - 10:30:05 PDT
