unanswered Martinize2 error in building the system

  • kesavan
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9 months 3 weeks ago #9671 by kesavan
Hi all,
I'm trying to convert an all-atom system having 100 chains of proteins bound with peptide using martinize2 version martinize with vermouth 0.9.1. But I ended up with the CG system built with seven molecule itp files. I previously tried with the apo state using the same command, but it worked well. I couldn't able to figure out the error. Could you help me in this regard?

martinize2 -f 1.pdb -o PRO_topol.top -x PRO_CG.pdb -ff martini3001
INFO - general - Read 2 molecules from PDB file 1.pdb
INFO - step - Guessing the bonds.
INFO - general - 7 molecules after guessing bonds
INFO - step - Repairing the graph.
INFO - general - Applying modification N-ter to residue -MET1

INFO - general - Applying modification mapping ('COOH-ter',)
INFO - general - Applying modification mapping ('COOH-ter',)
INFO - step - Averaging the coordinates.
INFO - step - Applying the links.
INFO - step - Placing the charge dummies.
INFO - step - Writing output.

Thank you


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