AMBER: How to check for water mediated hydrogen bonds?

From: Hannes Loeffler <hal.iam.u-tokyo.ac.jp>
Date: Mon, 28 Nov 2005 13:52:44 +0900

Hello everybody,

I know from the ptraj output that a residue A makes a hydrogen bond to
a solvent molecule with a certain occupancy and also a residue B is
hydrogen-bonded to a solvent. Now I would like to know whether a
single solvent molecule (or possibly a chain) bridges these two residues
or not. What would be a good way to check for water mediated hydrogen
bonds?

TIA,
Hannes. 

-- 
Hannes Loeffler | tel: +81-3-5841-1472 | fax: +81-3-5841-2297
http://www.hloeffler.info/ | mailto:hal->iam u-tokyo ac jp
Laboratory of Molecular Design, Institute of Molecular and Cellular
Biosciences, Center of Bioinformatics, University of Tokyo, Japan
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Received on Mon Nov 28 2005 - 05:53:02 PST
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