AMBER: analysing water behavior during MD

From: Vlad Cojocaru <>
Date: Fri, 13 Jan 2006 16:17:06 +0100

Dear amber users,

   I am interested to extract information about water from amber
trajectories... For example to identify possible water channels in a
protein or high occupancy water spots inside the macromolecule (having
the results represented as color maps drawn according to occupancy).
   I have never done this type of analysis and I was wondering if
anybody could point me to software that can do this or at least point me
to some references that describe such type of analysis..

Thank you very much in advance

Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
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Received on Sat Jan 14 2006 - 06:10:06 PST
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