Re: Keeping water out of the binding pocket with ColVar

From: Wang Yi (dexterwy_at_gmail.com)
Date: Fri Jul 20 2012 - 20:21:30 CDT

Yeah, I'd like to keep every water molecule out of the cavity.
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Yi (Yves) Wang
Duke University

On 2012-7-20, at 下午9:19, Aron Broom wrote:

> you could certainly do that, but the problem is, which water molecule? If you just have a distance restraint, you'd have to do it for each water... Perhaps there is a different colvar that would be better, I don't know.
>
> On Fri, Jul 20, 2012 at 9:14 PM, Wang Yi <dexterwy_at_gmail.com> wrote:
> Hi NAMD experts,
>
> I'm wondering if there's any way to keep the solvent out of the binding pocket of a receptor, to sort of create an empty cavity in a solvent box. I was thinking about using the "lower wall" feature, but not quite sure how to implement it. Or maybe there's better way to do it? Thanks.
>
> Best,
> ___________________________
>
> Yi (Yves) Wang
> Duke University
>
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> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>

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