AMBER: Calcium and GB

From: cailliez <Fabien.Cailliez.ibpc.fr>
Date: Tue, 08 Jun 2004 13:38:58 +0200

Dear Amber users,

I would like to run a molecular dynamics simulation on a protein, which
is complexed with calcium ions.
I wonder if I can do that using GB model as an implicit solvent
representation.
I saw that there are no particular GB parameters for calcium (as for
many other
atom types).

Is it correct to do a simulation with free ions and GB solvent ?
And if so, do I have to determine precisely GB parameters for Ca2+ (and
how can I do that) ?

Thank you in advance for your answers,
Fabien 

--
__________________________________________________________________
Fabien Cailliez                         Tel : 01 58 41 51 63
Laboratoire de Biochimie Théorique      e-mail : cailliez.ibpc.fr
IBPC    13, rue Pierre et Marie Curie
75005 Paris
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Received on Tue Jun 08 2004 - 13:53:00 PDT
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