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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
http://www.poissonboltzmann.org/
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pdd2pqr ligand problem #230

Closed kva0987 closed 2 years ago

kva0987 commented 2 years ago

Hi,

I encountered some issues while trying to run pdb2pqr for APBS.

  1. pdb2pqr cannot take am bond type from mol.2 file any more. I believe it was able to do that before.
  2. WARNING:PDB2PQR could not identify the following residues and residue numbers as returned by PROPKA or PDB2PKA WARNING:Can't find HETATM 627 1 N1 in MOL2 file It says it cannot find TETATM in mol2 file. So I used the same setup which used to work few months ago, but still giving the same error.

Could someone help on this?

kva0987 commented 2 years ago

Job ID is zfh7fqlmwo_20210930

jbardhan commented 2 years ago

Hello,

Thank you for alerting us to this, and for submitting the job ID!

Do you recall (even if only roughly) when you remember pdb2pqr being able to take the bond type from a mol2 file?

Thanks very much, Jay

kva0987 commented 2 years ago

I had ran pdb2pqr this February and May. I did not recognize this kind of error then.

jbardhan commented 2 years ago

Thank you! That's helpful.

Jay

sobolevnrm commented 2 years ago

@kva0987 Can you please provide the files you used with this calculation? I'm going to close the issue until you post them. Please feel free to reopen afterward. Thanks.