Re: [AMBER] error in cluster analysis by cpptraj

From: Daniel Roe <>
Date: Thu, 12 May 2016 08:21:48 -0600


The manual is often a good place to check for information. If you look
at the entry for the 'cluster' command in the cpptraj section of the
Amber manual (currently 29.10.4 on page 623 of the current Amber 16
manual) you will see that the '<mask>' argument is only for the
rms/srmsd/dme distance metrics. The output from cpptraj is telling you
as much:

On Thu, May 12, 2016 at 4:06 AM, Michael Shokhen
<> wrote:
> CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:111.OG,]) best-fit

If you want to cluster on data from a data set you need to use the
'data' keyword. There is in fact an example of this (using distance,
which is what you want) given in the manual:

distance endToEnd :1 :255
cluster data endToEnd clusters 10 epsilon 3.0 summary summary.dat info info.dat

So in summary you will need to have a distance command prior to cluster:

distance d0 :111.OG :164.NE2

then use that data set in your cluster command:

cluster data d0 ...

Hope this helps,


> Minimum pts to form cluster= 25
> Cluster distance criterion= 0.900
> Sieved frames will only be added back if they are within
> 0.900 of a frame in an existing cluster.
> (This option is more accurate and will identify sieved
> frames as noise but is slower.)
> Initial clustering sieve value is 20 frames.
> Cluster # vs time will be written to combined.cnumvtime.dat
> Cluster information will be written to
> Summary comparing parts of trajectory data for clusters will be written to split.dat
> Frames will be split at: 5000
> Error: [cluster] Not all arguments handled: [ :164.NE2 ]
> 1 errors encountered reading input.
> TIME: Total execution time: 0.1955 seconds.
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email:<>
> _______________________________________________
> 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)
AMBER mailing list
Received on Thu May 12 2016 - 07:30:04 PDT
Custom Search