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
>
>
>
> _______________________________________________
> AMBER mailing list
> 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
Received on Mon Nov 26 2012 - 09:00:02 PST
