These are negatively charged Calcium ions? That doesn't seem right. Anyway,
if you cannot find a reliable crystal structure, I have an algorithm to
place non-covalently interacting ions and water using statistical liquid
theory (3D-RISM). I have a tutorial in AMBER. In the manuscript I tested
Sodium ions but I have also unpublished successful results with Ca2+.
You can find information here: http://goo.gl/uLohs, and the tutorial here:
http://goo.gl/JilCq.
Let me know if you have further questions.
-Dan
On Fri, May 11, 2012 at 7:22 AM, Mahendra B Thapa <thapamb.mail.uc.edu>wrote:
> 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
> > --
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> _______________________________________________
> 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
--
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 10 2012 - 19:00:04 PDT
