Re: [AMBER] clustering error message

From: Daniel Roe <>
Date: Wed, 17 Oct 2012 14:08:02 -0600


For some reason all of your output in the email was jumbled together
(no newlines) so it was a little difficult for me to parse through.
You also didn't include all of the output, and I suspect there may be
other warnings.

> Read 11500 frames and processed 11500 frames.
> Warning: DataFile xxx: Set average contains no data - skipping.

This indicates that although your trajectory was processed, the
clustering command didn't save any frames, which in turn indicates
that for some reason initialization of the clustering command failed.
Can you send me off-list the entire output from cpptraj?

Also note that you seem to be using the 'ptraj' clustering syntax,
which is slightly different from cpptraj. Cpptraj does not have an
'average' option for coordinates output; cluster coordinate output
options are:

clusterout <trajfileprefix> [clusterfmt <trajformat>]: Output entire
clusters to <trajfileprefix>.c<cluster#>
singlerepout <trajfilename> [singlerepfmt <trajformat>] ]: Output
representative structure of each cluster to a single trajectory named
repout <repprefix> [repfmt <repfmt>]: Output representative structure
of each cluster to separate trajectory files named
<repprefix>.<cluster#>.<EXT>, where EXT is an extension based on
format specified by <repfmt>.

Also note that 'out' just writes cluster # vs frame. To get ptraj-like
cluster info, do 'info <infofile>'. Further information can be
obtained from 'summary <summaryfile>'. See the manual for more
complete details.

Currently ptraj clustering has far more options than cpptraj (most
notably 'sieve') so you may want to look at that as well.

Hope this is helpful.


On Wed, Oct 17, 2012 at 11:29 AM, Catein Catherine
<> wrote:
> Dear AMBER Experts,
> I tried to do clustering for my mdcrd files using the following cpptraj script:
> ------------------------------------------------------------------------------------------------------------------trajin ../mdcrd/xxx.mdcrdautoimagecluster out xxx average pdb averagelinkage clusters 10 mass rms .C1',CA------------------------------------------------------------------------------------------------------------------
> However, I got the following message in the cpptraj.log file.
> ----------------------------------------------------------------------------------------------------------------------- [xxx.mdcrd] (1-500, 1) ------- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

> ACTION OUTPUT:CLUSTER: CpptrajPairDist found, loading pairwise distances.Warning: TriangleMatrix::LoadFile: File (null) has 11500 rows, expected 0.
> DATASETS: There is 1 data set: averageDATAFILE OUTPUT: md0to27: averageWarning: DataFile xxx has no sets containing data - skipping.------------------------------------------------------------------------------------------------------------------
> What's wrong with my cpptraj script? Please help to point out my fault input files.
> Many thanks,
> Catherine
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Oct 17 2012 - 13:30:05 PDT
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