AMBER Archive (2006)

Subject: Re: AMBER: analysing water behavior during MD

From: Fabian Boes (
Date: Fri Jan 13 2006 - 10:22:01 CST

Hi ...

... have a look at this answer from Thomas Cheatham, maybe it's suited
to solve your problem:



Vlad Cojocaru wrote:
> 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
> vlad


Fabian Bös

Institute of Technical Biochemistry University of Stuttgart / Germany

Phone: +49-711-6857481 Fax: +49-711-6853196 Email:

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