Re: [AMBER] About clusterdihedral

From: Daniel Roe <>
Date: Thu, 21 Feb 2019 14:12:10 -0500


The 'clusterdihedral' command was only really ever intended for use
with "reservoir" replica exchange - the manual really needs to be
changed to reflect that.

If you want to cluster using dihedral angles you should use the
'cluster' analysis command with the 'data' keyword (examples:
$CPPTRAJHOME/test/Test_Cluster_DataSet/ If you're reading
the dihedral data in via 'readdata' make sure you let cpptraj know
that it's torsion data via 'dataset mode torsion <set names>' so it
knows the data is periodic.

Hope this helps,


On Thu, Feb 21, 2019 at 4:07 AM Gilberto Pereira
<> wrote:
> Dear Amber community,
> I apologize in advance if this is not the proper place to put this
> question.
> I have been trying to use the clusterdihedral function to cluster a
> trajectory of a ligand according to its three dihedral angles and I notice
> two things: The clustering process gives me almost 200 dihedrals if i use a
> default of 10 bins and the number of clusters varies wildly with bin
> number. Can you please indicate where i can find documentation explaining
> how the clustering is performed and how to properly use this tool? Sadly, i
> could not find the answer in the manual for Amber18.
> Thank you very much.
> Gilberto Pereira
> _______________________________________________
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Received on Thu Feb 21 2019 - 11:30:03 PST
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