[gmx-users] Number of waters

Xavier Periole Xavier.Periole at physbio.mssm.edu
Tue Sep 23 19:59:00 CEST 2003

There is no utilities I know in gromacs package that allows
you to do selections based on distances. For a analysis of
one snapshot you could use a basic visualization program
(Rasmol, VMD, Swisspdbviewer etc ...) and play with the
selection tools (water within a certain distance from both the
protein and the ligand). If you are interested in the evolution
of the interface with time you could download your trajectory
in VMD and also play with the selection tools. But I am not
sure that VMD is going to "refresh" the selection for each
snapshot rather than doing it on the first snapshot and follow
the selection along the trajectory. But I guess that if the water
molecules between your protein and your ligand are important
they would have a reasonable "life time". So if there is an exchange
of water you can see it easily on the screen and then include it in
your "selection".

Hope it'll help.

On Monday, September 22, 2003, at 09:14  am, Raj Badhan wrote:

> Hope someone can help.
> I would like to be able to calculate the number of water molecules
> berween the dimer interface of a protein.
> Any ideas of how this can be done?
> Many thanks
> Raj Badhan
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