AMBER Archive (2009)

Subject: Re: [AMBER] How to find water-mediated hydrogen bond?

From: Hannes Loeffler (hannes.loeffler_at_stfc.ac.uk)
Date: Thu Sep 03 2009 - 02:53:51 CDT

On Wed, 2009-09-02 at 22:10 +0800, Catein Catherine wrote:
> How to identify a water mediated hydrogen bond?
> drug-OH...solvent 80% 2.7A...
> solvent....HO-residueX 40% 3.0A...

If a water molecule mediates a H-bond I would think that the water has
to make H-bonds simultaneously to the other two partners. Your residueX
binds to solvent only 40% of the time (where does it bind to the other
60% of the time?) where solvent can be different molecules possibly
exchanging rapidly (check visually or compute residence times for
example). This may reduce the chance of being a mediating bond
considerably.

Also make sure that you do not have vanishing H-bonds. Even if you find
that your data supports your idea make sure that you have reasonable
long simulation times.

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