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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
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Swapped HD21/HD22 assignment for ASN #242

Closed chemsh closed 2 years ago

chemsh commented 2 years ago

Dear PDB2PQR authors,

we find ASN's HD21/HD22 atom labels are swapped when PDB2PQR guesses the missing hydrogens' positions. According to the original CHARMM forcefield topology, for example top_all36_prot.rtf, HD21 is cis to OD1 while HD22 trans. Please see attached an example of P450 (_pdb2pqr.pdb). In the resulting structure _pdb2pqr.out.pdb all ASN HD21 atoms are trans and HD22 have become cis. The two hydrogens bare a bit different charges of 0.32 and 0.30, respectively, so that Coulombic energy will be calculated with a deviation. We appreciate if you could take a look and fix the issue. Many thanks.

Kind regards,

You

chemsh commented 2 years ago

p450_pqd2pqr.tar.gz

sobolevnrm commented 2 years ago

Hi @chemsh -- thank you for reporting this. We will investigate.

chemsh commented 2 years ago

@sobolevnrm Brilliant! Thank you very much.