AMBER Archive (2009)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Mar 11 2009 - 09:33:38 CDT

Hi Sundar,

I suggest taking a look at the clustering section (section 6) in the
following tutorial: http://ambermd.org/tutorials/basic/tutorial3/

This will show you how you can plot the cluster id's against time etc so
that you can see when each cluster occurs etc.

Good luck,
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of S.Sundar Raman
> Sent: Wednesday, March 11, 2009 5:44 AM
> To: AMBER Mailing List
> Subject: [AMBER] Seeking for suggestion related to plot the cluster out
> file
>
> 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/prot_new1.dyn5.nc
> 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
> other.
> I am seeking for a help in this regard. Eagerly waiting for reply.
>
> with regards
> sundar
> --
> S.Sundar Raman
> CSIR-SRF
> Chemical Laboratory
> Central Leather Research Institute
> Adyar, Chennai, India- 600 020
> &
> DAAD Research Scholar
> EML
> Schloss-Wolfsbrunnenweg 33
> D-69118 Heidelberg
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

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