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normal BUG report in Martinize.py

  • Hezaveh
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9 years 9 months ago #3914 by Hezaveh
BUG report in Martinize.py was created by Hezaveh
Hello,

I'm running Martinize-2.4 to get CG model of my protein but it gives wrong output for Protein.itp. The problem only rise when there Unknown chains are detected among Protein chains then the program fails to perform properly and give wrong Protein.itp outputs. If one cut out the Unknown chains then program works again. Could you please solve this problem.

Thank you very much

Best,
Samira

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9 years 9 months ago #3915 by jaakko
Replied by jaakko on topic BUG report in Martinize.py
Hi Samira,

thanks for the bug report. It would help us greatly if with a bug report you could provide:
  • (link to) an example pdb where the problem arises
  • the exact command you used to run martinize
  • description of what exactly is wrong with the itp (and possibly the produced itp file and expected (correct) output)

Debugging these without sufficient data takes orders of magnitude longer.

- Jaakko

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9 years 9 months ago #3916 by Clement
Replied by Clement on topic BUG report in Martinize.py
If by "Unknown chain" you meant unknown residues in the structure, it makes sense the script stops, doesn't it? If people (X-ray, NMR) couldn't resolve it, how could we "fix" anything?

Either you modify it yourself (if the sequence is known, you can mutate the unknown residue to the good one with pymol for instance), either your remove it from the PDB file.

Nothing to do with martinize.py here...

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  1. Force Fields
  3. Proteins
  5. BUG report in Martinize.py
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