AMBER Archive (2009)
Subject: Re: [AMBER] ptraj cluster - snapshot number of a representative structure
From: Jianyin Shao (jyshao2004_at_gmail.com)
Date: Thu Aug 20 2009 - 10:50:22 CDT
I am afraid that information is not readily available in the output files.
After the trajin command reads in trajectories, sometimes skipping
snapshots, the cluster command does not know the snapshot numbering in the
original trajectory any longer. As you suggested, the best way to get this
information might be superimposing all snapshots on your representative
structures. Sorry for that bad news.
2009/8/20 Marcin Krol <mykrol_at_cyf-kr.edu.pl>
> After trajectory clustering in ptraj I get a representative structure for
> each cluster, which is a trajectory snapshot closest to the centroid of the
> cluster. I'd like to know the snapshot number in a trajectory, so that I can
> extract it again and I can't find this information. Is this info available
> I know I could superimpose all snapshots on the representative structure
> and find it in this way, but it's a bit tedious..
> many thanks
> Dr Marcin Krol
> Zaklad Bioinformatyki i Telemedycyny
> Collegium Medicum Uniwersytet Jagiellonski
> e-mail: mykrol_at_cyf-kr.edu.pl
> AMBER mailing list
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