Hi,
Ptraj log file shows that it read the crd file, but no output file in clustering using ptraj.
still shows a segmentation error
I browsed through,
Similar scripts reported without any error. but in my case it doesn't work.
Any help will be very much appreciated
Input script
trajin WTO.crd
#cluster out c-out representative pdb average pdb means clusters 10 rms :1-25
cluster out clusters/c20ns all amber representative pdb average pdb averagelinkage sieve 10 clusters 10 rms :1-25
Log file
PTRAJ: cluster out clusters/c20ns all amber representative pdb average pdb averagelinkage sieve 10 clusters 10 rms :1-25
WARNING: Error in mask string, no "." or ":" present (averagelinkage)
[No output trajectory specified (trajout)]
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 24000 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (WTO.crd) is an AMBER trajectory with 24000 sets
NO OUTPUT COORDINATE FILE WAS SPECIFIED
ACTIONS
1> AVERAGE: dumping the average of the coordinates to file pdb
start: 1 Stop [at final frame] Offset: 1
Atom selection [No atoms are selected]
Output file information: File (pdb) is an AMBER trajectory
Error file
Checking coordinates: WTO.crd
WARNING in dispatchToken: Token string "cluster" not found in tokenlist
WARNING in dispatchToken: Token string "out" not found in tokenlist
WARNING in dispatchToken: Token string "clusters/c20ns" not found in tokenlist
WARNING in dispatchToken: Token string "all" not found in tokenlist
WARNING in dispatchToken: Token string "amber" not found in tokenlist
WARNING in dispatchToken: Token string "representative" not found in tokenlist
WARNING in dispatchToken: Token string "pdb" not found in tokenlist
/var/spool/torque/mom_priv/jobs/677156.santa.SC: line 15: 19593 Segmentation fault ptraj 001.top < ptrajclus.in > logWTOclus
Thanks,
Mannan
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Received on Tue May 21 2013 - 04:00:03 PDT
