Re: [AMBER] Trajectory Clustering

From: Daniel Roe <>
Date: Fri, 26 Oct 2012 08:22:05 -0600


This information is in [outfile].txt. The first part of this file will
contain some general information about the clustering algorithm used
and some stats on the clusters themselves. Then there will be a line

#Clustering: <X> clusters

where X is the total number of clusters, followed by X lines
specifying which frames belong to that cluster. For example, say you
have 3 clusters and 5 frames; you may get something like:

#Clustering: 3 clusters

In this case frame 1 is in cluster 3, frames 2-3 are in cluster 1, and
frames 4-5 are in cluster 2.

If you use cpptraj, cluster number vs time is printed to the 'out
<file>' by default. However, cpptraj clustering does not currently
have all of the features of ptraj clustering.

Hope this helps,


On Fri, Oct 26, 2012 at 6:08 AM, Chiara Pallara <> wrote:
> Hi,
> I clustered the frames of my trajectory into 10 clusters with the
> command cluster of ptraj module.
> I applied the averagelinkage algorithm on the alpha carbons of my sistem
> using this command:
> cluster out [outfile] representative pdb average pdb averagelinkage
> clusters 10 rms .CA
> Now I would to know the MD times of the each cluster representative and
> its members. Do you know where I can find this information? I did not
> find nothig about in the output file.
> Thanks
> Chiara
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Oct 26 2012 - 07:30:03 PDT
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