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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Received on Mon Nov 26 2012 - 05:30:03 PST
