Dear Dr. Daniel
The protein is 2BCA which binds two Ca- atoms [ the structure is
determined with nmr technique], I wish to know to find the coordinates of
these two Ca- atoms { The crystallographic structure of this protein is
also available but I am interested in nmr structure.}. There are few lines
about these in a paper by "Sylvie Marchand and Benoit Roux" but
unfortunately I did not understand because of brief explanations. If there
are related papers with some detailed explanations , please let me know.
Thanks,
Mahendra Thapa
On Mon, Apr 30, 2012 at 9:49 PM, Thapa, Mahendra (thapamb) <
thapamb.mail.uc.edu> wrote:
>
>
>
> ________________________________________
> From: Daniel Sindhikara
> Sent: Monday, April 30, 2012 7:48:44 PM (UTC-06:00) Central America
> To: AMBER Mailing List
> Subject: Re: [AMBER] getting metal ions coordinates of nmr structures of a
> protein
>
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Dr. Daniel J. Sindhikara
> Ritsumeikan University
> E-mail: sindhikara.gmail.com
> Website: goo.gl/fLAqx
> --
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> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Thu May 10 2012 - 15:30:03 PDT
