Running into error with .runJob

[bvelasq]

Hello, I've been attempting to use PyContact to run some analysis on psf and pdb files generated in VMD, and I went through the tutorial with the GUI just fine using the rpn11_ubq files. However when I attempted to use your example script, automation.py, I ran into this error:

[bv1@xyz ~]$ python PyCo_example.py Running job: attemptPdbDcd1 on 4 cores. Traceback (most recent call last): File "PyCo_example.py", line 5, in job.runJob(4) File "/home/bv1/anaconda2/lib/python2.7/site-packages/PyContact/core/Scripting.py", line 33, in runJob self.analyzer.runFrameScan(ncores) File "/home/bv1/anaconda2/lib/python2.7/site-packages/PyContact/core/ContactAnalyzer.py", line 72, in runFrameScan raise Exception Exception

I double checked that my processor had 4 cores before hand, and I ran tests with the core value from 1 to 4 so I am unsure where the error is occuring and I am unsure what is causing the exception to be raised. Any help is appreciated, thanks!

[maxscheurer]

Hi,

could you supply the full PyCo_example.py script you are using? Sorry that the exception handling is not really clear, but I'm sure it has nothing to do with the core number. The program fails downstream, most likely through the atom selections or the input files supplied.

[bvelasq]

Sure thing

from PyContact.core.Scripting import PyContactJob, JobConfig

job = PyContactJob("/home/bv1/Desktop/rpn11_ubq.psf", "/home/bv1/Desktop/rpn11_ubq.dcd", "attemptPdbDcd1", JobConfig(5.0, 2.5, 120, [0,0,1,1,0], [0,0,1,1,0], "segid UBQ", "segid RN11"))

job.runJob(4)

job.writeSessionToFile()

[bvelasq]

Hello,

Just an update, apparently I put segid RP11 instead of segid RN11 so the selection text for selection 2 was incorrect. The issue is fixed, however I was having similar problems with another script but those seem to have resolved themselves. Thanks!