[Chimera-users] Waters of hydration in a protein

Elaine Meng meng at cgl.ucsf.edu
Tue Oct 26 09:24:01 PDT 2010

Hi John,
I had some suggestions after your similar question earlier this year,

... those generally provide some analysis of which waters are H-bonding at any given time.  

If you wanted to follow a particular water residue through time, you could select it and then indicate in FindHBond (or using similar options of findhbond command) to restrict the calculation to only H-bonds of that water, then run the same calculation at different time steps.

The only other idea I have is maybe to use the "occupancy" map calculation capability of MD Movie.  This  would be more appropriate for tracking probable locations of water oxygens or hydrogens over the whole trajectory than for following one water at a time.   That is described here
... and also used in this tutorial

Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 26, 2010, at 8:04 AM, Beale, John wrote:

> I am conducting molecular dynamics simulations on a protein in explicit water. I would like to be able to determine the positions of waters of hydration of the protein at the beginning and then at various points along the MD trajectory. What I need to do is locate the position of a water molecule that is hydrogen bonded to a given amino acid and somehow tabulate the positional data.
> Is there a way to do this in Chimera?
> Thanks!
> John M. Beale, Jr., Ph.D.
> Professor of Medicinal Chemistry and Pharmacognosy
> Saint Louis College of Pharmacy
> 4588 Parkview Place
> Saint Louis, Missouri  63110
> 314-446-8461
> Cell: 314-315-0409
> FAX: 314-446-8460
> jbeale at stlcop.edu
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