Re: Keeping water out of the binding pocket with ColVar

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Jul 20 2012 - 23:44:19 CDT

Try tclbc forces. See the user-defined forces tutorial.

On Jul 20, 2012, at 8:21 PM, Wang Yi wrote:

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