Hi Dan,
Thanks very much for your prompt answer. I tried it as you suggested. The
clustering in cpptraj goes well - there is no segfault as with ptraj.
However, as far as I know, clustering with ptraj is preferred as ptraj
offers more options and a branch of methods that are not yet available in
cpptraj. Therefore, your possible help with ptraj would be very
appreciated.
Best wishes,
Adam Jarmula
> Hi,
>
> Unfortunately a segfault is difficult to debug without being able to
> reproduce it. Could you try the clustering with cpptraj and see if you
> still get a segfault? Note the syntax is slightly different. You will want
> something like:
>
> cluster out iab6.dat summary iab6.summary.dat info iab6.info repout
> iab6.rep repfmt pdb clusterout cluster.nc clusterfmt netcdf averagelinkage
> clusters 3 mass .CA
>
> iab6.dat: Will contain cluster # vs time.
> iab6.summary.dat: Will contain a brief summary of each cluster (# frames,
> avg dist, centroid, etc).
> iab6.info: Will contain ptraj-like cluster output
> iab6.rep.cX: Will contain representative structure for cluster X in PDB
> format
> cluster.nc.cX: Will contain entire cluster X in netcdf format. This can be
> used to generate avg structure if needed (cpptraj has no 'average' keyword
> for clustering).
>
> In the meantime, I will try to reproduce the issue with a similar-sized
> system (6 aa, 6000 frames).
>
> -Dan
>
> On Mon, Nov 26, 2012 at 6:25 AM, <adarm.nencki.gov.pl> wrote:
>
>> Dear Amber users,
>>
>> I got a problem with clustering with ptraj from AmberTools12. I work
>> with
>> two small peptides containing respectively 5 (iab5) and 6 (iab6) amino
>> acids. The problem concerns only the larger peptide from the two since
>> for
>> the smaller one everything goes smooth. The trajectory of molecular
>> dynamics contains 6000 structures from a 30 ns run. When I try to do the
>> clustering, segmentation fault occurs and ptraj crashes. My cluster
>> command looks like:
>>
>> cluster out iab6 representative pdb average pdb averagelinkage clusters
>> 3
>> rms mass .CA
>>
>> First, the PairwiseDistances are calculated and saved to the disk. Then,
>> after some fairly long time (about two hours), the ClusterMerging.txt
>> file
>> is generated and dumped to the disk. Till this moment the program
>> reports
>> no problems at all. However, it is then when ptraj crashes upon
>> attempting
>> to "Aligning the most representative frames from each clusters to
>> cluster
>> 0". I tried the calculation on two different computers, with the same
>> result in both cases. Would be grateful for help.
>>
>> Thanks in advance,
>> Adam Jarmula
>>
>>
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Nov 26 2012 - 13:30:02 PST
