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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
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Ligand with Amide Bonds #325

Closed GeorgianaLiang closed 1 year ago

GeorgianaLiang commented 1 year ago

Dear pdb2pqr developers: I am looking to assign charges to a receptor considering the ligands bound to the receptor. I collected the needed files from PDB. However, the program tells me that the ligand (NAG) has an amide bond, which is not accepted by the program. Is there a way to go around this constraint? Thank you so much in advance!

sobolevnrm commented 1 year ago

Can you please provide more information about your structure (ideally a PDB file) as well as the exact error message you are receiving from PDB2PQR?

Thank you

GeorgianaLiang commented 1 year ago

I was using the PDB file 5kxi from the PDB website (with the sodium and nicotine removed). The problem arise with the NAG ligand (I converted from PDB to mol2 using a third-party program). The exact error message is "NotImplementedError: PDB2PQR does not currently support the amide (am) bond type".

sobolevnrm commented 1 year ago

image

Because the NAG ligand contains an amide bond, PDB2PQR will not be able to assign charges to it. I recommend removing that ligand from the structure.