Why don't you simulate the protein in (explicit, obviously) water
environment and compute the residence time for water molecules within
the area of interest? Will take a longer time, but looks (to me) more
interesting approach....
hth,
--Alessandro
On Fri, Oct 23, 2009 at 10:23 AM, Vlad Cojocaru
<Vlad.Cojocaru.eml-r.villa-bosch.de> wrote:
> Dear Amber users,
>
> Does anyone know a software (free for academics) to hydrate protein pockets
> ? To be more precise, I am interested in a program that can use the force
> field parameters (amber or other) and calculate favorable positions of
> waters inside close pockets in proteins or other types of molecules ...
>
> Thanks for any suggestions
> Best wishes
> Vlad
>
> --
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>
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>
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> Fax: ++49-6221-533298
>
> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
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--
[ ]s
--alessandro
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Received on Fri Oct 23 2009 - 06:00:06 PDT
