Re: [AMBER] Cluster RMSD

From: Daniel Roe <>
Date: Fri, 3 Oct 2014 08:15:58 -0600


What you're talking about doing is more like filtering than clustering
(the latter is grouping things together via a distance metric and is
implemented in the 'cluster' analysis command). You can do what you
want in cpptraj in one of two ways:

The 'filter' command will allow only frames that match certain
criteria to be processed by subsequent actions. For example, given the

rmsd R0 first .CA
filter R0 min 0.5 max 1.0 out filter.dat
distance d0 :1 :2

the 'distance' command (and any subsequent commands) will only be
processed if the data in the RMSD data set R0 is between 0.5 and 1.0.
Similarly, you can also use the 'outtraj' command to generate
trajectories with frames that match certain criteria:

rmsd R0 first .CA
outtraj netcdf maxmin R0 min 0.5 max 1.0

This will create a netcdf trajectory named that will
contain only frames with R0 in between 0.5 and 1.0.

Hope this helps,


On Fri, Oct 3, 2014 at 3:48 AM, Soumendranath Bhakat
<> wrote:
> Dear Ambersits;
> I need to cluster the snapshots within the range of RMSD 0.5 angstrom 1.0
> angstrom.
> Is there any cluster command which can produce a .dat or .agr file which
> can cluster snapshots within the range of 0.5 angstrom and 1.0 angstrom .
> Any help regarding this will be highly appreciated.
> Regards;
> SB
> --
> Thanks & Regards;
> Soumendranath Bhakat
> Researcher
> Molecular Modelling and Drug Design Research Group
> Discipline of Pharmaceutical Sciences
> UKZN, Westville
> Weblink:
> Past: Department of Pharmaceutical Sciences
> Birla Institute of Technology, Mesra, India
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Oct 03 2014 - 07:30:04 PDT
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