VMD-L Mailing List

From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Sat Apr 15 2006 - 19:15:26 CDT

Hello John,
Thank you. That's what I'd like to try.
Also, is there a way to get the potential of mean force between two
residues using VMD?
Thanks.
Margaret

On Sat, 15 Apr 2006, John Stone wrote:

>
> Margaret,
> Are you trying to identify waters enclosed in internal cavities, or
> are you looking for something waters near specific residues?
>
> The latter case is simpler as you could do something like:
> water within 5 of (residue 5 6 7 38 49)
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sat, Apr 15, 2006 at 05:54:25PM -0400, Margaret Shun Cheung wrote:
>>
>> Dear VMD wizards,
>>
>> I am struggling with the tcl syntax (VMD tkconsole).
>> I'd like to select water molecules between two residues in a trajectory
>> (eg 100 frames).
>>
>> The "within 5 of protein" seems to only select waters around proteins. But
>> how could I identify water molecules that are enclosed between two or more
>> residues?
>> Thank you very much for your help!
>> Sincerely,
>>
>> Margaret S. Cheung,
>> Ph. D. Postdoctoral Fellow,
>>
>> ------------------------------------------------------------
>> Room 2117 Tel: (301) 405-4892
>> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
>> University of Maryland http://glue.umd.edu/~mscheung
>> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
>> ------------------------------------------------------------
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>

Margaret S. Cheung,
Ph. D. Postdoctoral Fellow,

------------------------------------------------------------
Room 2117 Tel: (301) 405-4892
Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
University of Maryland http://glue.umd.edu/~mscheung
College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
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