[Chimera-users] Waters of hydration in a protein

Beale, John John.Beale at stlcop.edu
Tue Oct 26 08:04:40 PDT 2010

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?


John M. Beale, Jr., Ph.D.
Professor of Medicinal Chemistry and Pharmacognosy
Saint Louis College of Pharmacy
4588 Parkview Place
Saint Louis, Missouri  63110
Cell: 314-315-0409
FAX: 314-446-8460
jbeale at stlcop.edu<mailto:jbeale at stlcop.edu>

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