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Problems with PDB2PQR when running APBS

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This FAQ applies to: Any version.

What to do if you get error messages in pdb2pqr package.

When running APBS, PMV uses pdb2pqr package to convert pdb to pqr before passing it to APBS. This package - located under MolKit folder - might not be up to date. If you see an error message similar to this one:

  File "./MolKit/pdb2pqr/routines.py", line 803, in repairAA
raise ValueError, text
ValueError: Unable to repair ASN 17 C

run the same molecule through PDB2PQR Server - http://nbcr.net/pdb2pqr. Read pqr generated by the latest pdb2pqr instead of the original pdb and PMV should be able to handle it.

You can also generate pqr with PMV (File → Save → Write PQR) after adding charges (Edit → Charges  → Compute Gasteiger) and radii (Edit → Atoms → Assign Radii).

by Sargis Dallakyan last modified 2008-01-03 17:41 Molecular Graphics Laboratory, TSRI

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