VMD-L Mailing List
From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Fri May 18 2012 - 06:26:55 CDT
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Dear Wendy,
You could calculate the "solvent accessible arrea" for every water
molecule (considering the solvent all the other waters).
Define a threshold for this and select those waters that are below this
threshold ..
If you have more cavities, you can do an additional step and select from
the selected waters those that are closed to the residues defining your
cavity of interest ...
Just an easy example ...
Vlad
On 05/18/2012 11:46 AM, Wendy González wrote:
> Dear VMD Users:
>
> I would like to calculate the amount of waters enclosed in an internal
> cavity of a protein during MD simulations.
> Do you have any tip?
> Thanks in advance,
> Wendy
-- Dr. Vlad Cojocaru Max Planck Institute for Molecular Biomedicine Department of Cell and Developmental Biology Röntgenstrasse 20, 48149 Münster, Germany Tel: +49-251-70365-324; Fax: +49-251-70365-399 Email: vlad.cojocaru[at]mpi-muenster.mpg.de
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