Re: [AMBER] clustering the trajectories

From: Esam Tolba <>
Date: Wed, 17 Oct 2012 21:49:09 +0200

Thanks for the note
                I am using the this command for clustering
cluster out ***** representative pdb average pdb averagelinkage clusters 5
I got as output three files for each cluster but the average and the
represintative files are empty and there is no error in the output file
*Best Regards,
Esam *

On Wed, Oct 17, 2012 at 3:26 PM, David A Case <>wrote:

> On Wed, Oct 17, 2012, Esam Tolba wrote:
> > > See the 'cluster' command for ptraj or cpptraj. Note that currently
> > > ptraj clustering has far more options than cpptraj. Refer to the
> > > AmberTools manual for more details.
> > How to use the 'cluster' command?
> > and what would be the output files?
> We expect users to invest a fair amount of effort before asking people on
> the
> list to spend their time in replies. People are willing to help for
> reports
> like "I read Section xxx of the manual, but I don't understand this
> sentence...", or "I tried the following calculation, but I got a strange
> result....". [Even better is with the addition: "I searched the Amber mail
> archives and Googled the error message, but could not find the help I
> needed."]
> Just asking people on the list to tell you what is already in the Reference
> Manual is not a good use of anyone's time.
> ...dac
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Received on Wed Oct 17 2012 - 13:00:02 PDT
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