From owner-chemistry@ccl.net Thu Sep 29 08:51:00 2011
From: "Thomas Cheatham tec3*o*utah.edu" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: How can I do cluster analysis or similarity analysis
Message-Id: <-45551-110929013316-25268-5s0h/w8IAthsSxOVBjp/GQ++server.ccl.net>
X-Original-From: Thomas Cheatham <tec3(~)utah.edu>
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Date: Wed, 28 Sep 2011 23:33:09 -0600 (Mountain Daylight Time)
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Sent to CCL by: Thomas Cheatham [tec3-#-utah.edu]

>  I did a molecular dynamics simulation with AMBER, and I saved a 
> thousand conformations during this run. I wish to do some cluster 
> analysis, or similarity analysis on the conformations I saved. I think 
> all the conformations can be groups into two main groups, because I see 
> the structure changes from one conformation to the other in the MD 
> simulation.

AMBER has an active mailing list and an archive at http://ambermd.org 
which would be a good place to search/ask about MD simulations with AMBER.

With the freely available AmberTools suite of programs are trajectory 
analysis capabilities to do clustering.  I am most familiar with ptraj 
which can cluster based on RMSd, distance-matrix, dihedrals, etc.  

Routinely we cluster based on RMSd.  There are many options, but a basic 
script to ptraj would be something like:

  trajin traj.strip

  cluster out clusters/c10 all none representative pdb average pdb \
    averagelinkage sieve 250 clusters 10 rms

In your case, you can cluster all frames (sieve 1) and to decide on the 
number of clusters I would visualize a 2D RMSd plot since 1D-RMSd plots 
can be deceptive with respect to cluster count.

See the manuals at http://ambermd.org for more information.  A paper 
describing that implementation is Shao et al. (Cheatham), JCTC ~2007.

Alternatives include MMTSB, tools distributed with GROMACS and 
GROMOS, and likely things builtin to NAMD and CHARMM.

If you get stuck, e-mail me off-list.

--tec3