Comparison against standard propka call fails (HETATM issue)

[IAlibay]

This is an upstream issue, but probably should be documented whilst the MDA parser has this current behaviour.

Expected

Passing a PDB to propka or propkatraj should give the same predicted pkas

Actual outcome

When passing 4LYI (everyone's favourite BRD4 model), the results will differ significantly for GLU 151, 154, and 163.

The cause for this is that the MDA PDBWriter will output everything with ATOM records whilst the native PDB has HETATM entries for the small molecules/ions/solvent. This causes the difference in results seen here (manualy hand-editing the output of a MDA PDBWriter file for 4LYI makes things work again).

I'm not versed enough in the internal workings for propka 3.1+ to know why HETATM and ATOMS are handled differently, maybe @orbeckst has more insights here?

[orbeckst]

Don't know off the top of my head but PROPKA 3 can deal with ligands and they are probably indicated by HETATM entries.