AMBER Archive (2008)

Subject: Re: AMBER: Help...which commands in ptraj does clustering by RMSD?

From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Thu Sep 11 2008 - 15:39:44 CDT

Jose,
I had exactly the same problem very recently. ptraj in Amber 9 doesn't
have this feature - you need to get AmberTools. That version has the
clustering capability.

Sasha

Jose Borreguero wrote:
> Dear Amber users,
> I am reading the Amber9 manual and I can't find the ptraj command to
> cluster the frames in a trajectory by mutual RMSD. Can anyone please
> tell me what is the command?
> Many thanks
> --
> Jose M. Borreguero
> Postdoctoral Associate
> Oak Ridge National Laboratory
> P.O. Box 2008, M.S. 6164
> Oak Ridge, TN 37831
> phone: 865-241-3071 fax: 865-576-5491
> Email: borreguerojm_at_ornl.gov <mailto:borreguerojm_at_ornl.gov>

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