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jensengroup / propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
http://propka.org
GNU Lesser General Public License v2.1
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Warning message: Unexpected number (15) of atoms in residue ASN 9 _ in conformation 60A #144

Closed mmerlini87 closed 2 years ago

mmerlini87 commented 2 years ago

I'm running some pKa calculations using propKa for a protein and for the same protein in a water environment. When I use only the protein the code is running fine while in the presence of the water molecules the code is returning the following warning message:

Unexpected number (15) of atoms in residue ASN 9 _ in conformation 60A

Looking at the code it seems that propKa is reading an inconsistent number of atoms for all the residues. Could you please explain me what is the reason of this warning? Could it be that it is due to the fact that the protein is already protonated?

sobolevnrm commented 2 years ago

Can you please share the PDB file that is causing the problem?

mmerlini87 commented 2 years ago

Hi,

here it is the PDB file causing the warning:

frame0-WAT.pdf

sobolevnrm commented 2 years ago

@mmerlini87 -- this is not converting to text cleanly. Could you please post the PDB as a .txt or .zip file?

sobolevnrm commented 2 years ago

I'm going to close this until we get a workable version of the PDB file.