Subject: Re: CCL:clustering database molecules

From: Anton Feenstra <feenstra)at(chem.vu.nl>
Date: Thu, 06 Nov 2003 17:50:57 +0100

Joey Harriman wrote:

> Hi,
> 
> I am trying to cluster a database of a tetrapeptide with different geometries.  I am
> currently using MOE and have tried varying fingerprints (at the 99%) threshold with no
> success.  Does anyone have a good system for clustering different geometries of the
> same molecule from a database?  Thanks in advance for any help you can offer.

There is a tool in the Gromacs (free under GPL at www.gromacs.org) package
desinged to cluster conformations from an MD trajectory. It will accept
concatenated .pdb files (all of the same molecule) as if it was a trajectory.
It is called g_cluster and has several algorithms to cluster conformations\
based on their RMSD, or you can read an externally generated 'difference'
matrix for your conformations.

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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