VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 12 2009 - 16:14:30 CDT

Hi,
  You can't control it with that much specificity, in particular with
regards to the atom count. You might look at some of the other solvation
tools out there and see if any others give you control over the exact
count of waters added.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 12, 2009 at 04:02:33PM +0800, pxq ?????? wrote:
> Hello everyone,
>
> I am trying to add water molecular to a trans-membrane-protein system, the question is can we control the total number and distribution of the solvate molecular (the water molecular to be added) with WMD. (Say, I want to add 5 water/lipid within 5A of the P atom)
>
> Any suggestion is greatly welcomed
>
> Best wishes
>
> Xueqin
>
>
>
> ================================================================================
> Pang Xueqin
> State Key Laboratory of Molecular Reaction Dynamics
> Dalian Institute of Chemical Physics
> Chinese Academy of Sciences.
> Tel: +86-411-84379352 Fax: +86-411-84675584
> E-mail: pxq_at_dicp.ac.cn
>
> =================================================================================
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078