Re: AMBER: Potential of mean force: how to extract the min structure?

From: <>
Date: Tue, 18 Sep 2007 10:09:29 +0200

A good way to do this is to analyse your mdcrd file with a visual
program, like vmd for example. Then you just pick some structures for
further analysis.
Otherwise, you can dump the pdb files from your mdcrd and pick the
interesting snapshots directly.
Good luck.

On Tue, 2007-09-18 at 15:39 +0800, Catein Catherine wrote:
> Dear Sir/Madam,
> A potential of mean force calculation has been done by varying the
> binding distances between receptor and a ligand. A minimum at a
> binding distance of 3 A was found according to WHAM result. I could
> like to extract the structures corresponding to this minimum for
> further analysis, e.g. flipping of neighbor residues and PBSA
> analysis. Could you please kindly instruct me if I can do it with the
> mdcrd files obtained at the window where min (3 A) was located? If
> not, what should I do to extract the min structure for further
> analysis?
> Best regards,
> Cat.
> ______________________________________________________________________
> Explore the seven wonders of the world Learn more!
Jerome Golebiowski, PhD
LCMBA, team Chemometrics and Molecular Modeling
University of Nice, parc Valrose
06108 Nice Cedex2 France
tel : +33 (0)4 92 07 61 03
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Received on Wed Sep 19 2007 - 06:07:32 PDT
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