On Mon, May 19, 2003, Javier Cuervo wrote:
>
> How can I deal with proteins that has Calcium ions (Ca2+), It seems to me
> that some forcefield (amber99) has parameters for it (C0), but I have not
> been able to produce a .top or .crd files using leap.
>
(1) You don't say what things you tried, and what happened as a result.
(2) Basially, you have to create a UNIT in LEaP that gives you what you
want. This might be a bare calcium ion (for that, see examples in
$AMBERHOME/dat/leap/lib/ions94.cmd, and create Ca2+ in an analogous way);
or, you might want a hydrated ion, treating the calcium and its first
solvation shell waters as a "molecule". An example of this is here:
%A V. Tsui
%A D.A. Case
%T Calculations of the Absolute Free Energies of Binding between RNA and Metal
%Ions Using Molecular Dynamics Simulations and Continuum Electrostatics
%J J. Phys. Chem. B
%V 105
%P 11314-11325
%D 2001
(3) Note that simulating divalent ions is *not* a standard piece of molecular
mechanics repertoire, which is partially why there are no pre-defined
residues. You might want to look at this:
%A T. Dudev
%A C. Lim
%T Principles Governing Mg, Ca, and Zn Binding and Selectivity in Proteins
%J Chem. Rev.
%V 103
%P 773-788
%D 2003
...good luck...dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Tue May 20 2003 - 15:53:02 PDT
