FAQs

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).