What metal is it? Do you know the coordinating sidechains? If so you might
have to place it by hand then optimize using QM. Included in AMBER is MCPB
which lets you build metal parameters using a bonded model. Use that to set
your system up once you have a reasonable starting geometry.
-Dan
On Tue, May 1, 2012 at 8:11 AM, Mahendra B Thapa <thapamb.mail.uc.edu>wrote:
> Dear AMBER users,
>
> Excuse me if my question is out of the
> purpose of posting in amber mailing list.
> pdb file of NMR structure of a metal binding protein does not contain
> coordinates of the metal ions that the protein binds. How to get the
> coordinates of the metal ions ?
>
> Thanks,
> Mahendra Thapa
> University of Cincinnati, OH
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>
--
Dr. Daniel J. Sindhikara
Ritsumeikan University
E-mail: sindhikara.gmail.com
Website: goo.gl/fLAqx
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Received on Mon Apr 30 2012 - 19:00:03 PDT
