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Hello Chris--
> So now I'm trying to finish running the pasd/cvn tutorial. I've submitted the
> job using the quick flag and everything runs well until the refine.py command
> is implemented in the runPASDquick script,
>
> xplor -quick -py refine.py -parallel -machines ${PBS_NODEFILE} > refine.py.out
>
> At this point my job terminates. I checked the refine.py.out file which
> contained this,
>
> refine.py(59): protocol.loadPDB("./cvn_pass3_avg.pdb")
> loading pdb file: ./cvn_pass3_avg.pdb?? [psf]PDBTool:read: atom not found in
> structure:? LEU 36 O
> ?matchInexactAtomEntry: matching entry??????? 36 O to atom? 36 OT1
>
It seems like the input file (cvn_pass3_avg.pdb) was truncated at resid
36. Did you run out of disk space?
> refine.py(83): refRMSD = create_PosDiffPot("refRMSD","name CA or name C or
> name
> N",
> refine.py(84):???????????????????????????? pdbFile='./cvn_reference.pdb',
> refine.py(85):???????????????????????????? cmpSel="not name H*")
> Exception: len(selection) [108] != len(selection2) [303]
This is due to the size difference between the input and reference
structures.
best regards--
Charles
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