Re: [AMBER] cluster using ptraj

From: Massimiliano Porrini <>
Date: Wed, 16 Feb 2011 12:42:59 +0000


What you call "clust_out.rep.c0" is the closest structure to the
cluster 0 centroid
(you named it cluster 1).

What I would do to catch the frame related to this structure is to calculate
and plot the RMSD with this structure as reference, e.g. for the backbone atoms:

trajin "mdcrd_file"
reference clust_out.rep.c0
rms reference mass out "rms_file.out" .C,CA,N

>From the graph you should get an RMSD = 0 only for one structure,
this is the frame you are looking for.

Probably there is a faster and simpler way to do that.


2011/2/16 475649770 <>:
> Dear professors:
>     I clustering my system using the ptraj module, and the program produced the file like "clust_out.rep.c0" as the represent structure of the cluster 1. I wanted to know that which snapshot this structure extracted from. I think this represent structure is the centroid of the cluster 1, I want to know which snapshot it is at the MD trajectory.
>     Thank you!
> _______________________________________________
> AMBER mailing list

Dr Massimiliano Porrini
P. E. Barran Research Group
Institute for Condensed Matter and Complex Systems
School of Physics & Astronomy
The University of Edinburgh
James Clerk Maxwell Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JZ
Tel +44-(0)131-650-5229
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Received on Wed Feb 16 2011 - 05:00:02 PST
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