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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
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Problems with Mn ion in enzyme #333

Closed mverissi closed 1 year ago

mverissi commented 1 year ago

Hi all,

I am trying to use the pdb2pqr server to prepare a polymerase which has one ligand (a deoxy-triphosphate) and three metal ions (2 Mn2+ and 1 Mg2+) in its active site (PDB code 5omf). I have exported the DTP and the two metal ions to a MOL2 file, but I get the following error when the pdb2pqr server starts the ligands' parametrization:

KeyError: "Unable to find radius parameter for self of type Mn in radius dictionary: {'C': 1.87, 'H': 1.1, 'O.co2': 1.76, 'N': 1.4, 'S': 2.15, 'F': 2.4, 'Cl': 1.82, 'I': 2.65}"

Is it possible to run pdb2pqr for this enzyme? I am attaching the enzyme and ligand files to this post (with a txtsuffix added, since Github doesn't accept mol2 or pdb files as attachments), as well as the pdb2pqr.stderr.txt file, in the hope it helps.

Best regards,

Marcos Verissimo Alves Lund University

pdb2pqr.stderr.txt 5omf_noligs.pdb.txt ligands.mol2.txt

sobolevnrm commented 1 year ago

We do not currently support the Mn ion. You could try to add it to PDB2PQR using the instructions in the documentation; however, please be aware that this will only add the charge contribution to output PQR file and will not influence the titration process, etc.