AMBER Archive (2009)

Subject: [AMBER] Seeking for suggestion related to plot the cluster out file

From: S.Sundar Raman (
Date: Wed Mar 11 2009 - 07:44:17 CDT

Dear amber users,
I am trying analyse the output of clustering. I used the following commands
in the ptraj to do clustering.

trajin /data/mcm/subramsn/simulation/prot/
strip :WAT
rms first mass :1-367 name rmsd
cluster out prot_cluster representative pdb average pdb means clusters 5 rms_at_CA

I got the following output files.
five cluster average structure files
five cluster representative files
five cluster trajectory files
one cluster.txt file
As i read from the research article I can understand the centroid values of
each cluster.
I would like to draw a plot from cluster.txt file as how each cluster is
distributed in the trajectory and how one cluster is different from the
I am seeking for a help in this regard. Eagerly waiting for reply.

with regards

S.Sundar Raman
Chemical Laboratory
Central Leather Research Institute
Adyar, Chennai, India- 600 020
DAAD Research Scholar
Schloss-Wolfsbrunnenweg 33
D-69118 Heidelberg
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