AMBER Archive (2009)

Subject: Re: [AMBER] software to hydrate protein pockets

From: Alessandro Nascimento (al.s.nascimento_at_gmail.com)
Date: Fri Oct 23 2009 - 07:50:05 CDT

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_at_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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-- 
[ ]s

--alessandro

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