AMBER Archive (2009)

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

From: S.Sundar Raman (sundar02_at_gmail.com)
Date: Wed Mar 11 2009 - 09:57:40 CDT

Dear Ross,
Thanks for your reply.
I find significant difference between the cluster.txt which i attached with
this mail with the one they showed in the tutorial.
In the tutorial ( which is version amber9 with *MMTSB Toolset) * the
distance from the centroid is given and i did not find such information in
my file ( amber tools 1.2 version). On the other hand in my file with
respect to time it give which group of cluster is exist.

therefore I am seeking for help to plot from this file
with regards
sundar

On Wed, Mar 11, 2009 at 3:33 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

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

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