plf.display_residues(protein_mol)

[milenamlakic]

I have a problem with plf.display_residues(protein_mol). There are a lot of O2-, don't know how to fix, if you have idea I would be grateful..

[cbouy]

Hi,

a few questions which might explain why this is happening:

• does your input file contain all hydrogen atoms explicitly? ProLIF requires all hydrogen atoms to be present
• does your input file contain any bond information? If you're reading from a PDB file, it's quite possible that only the ligand has them (or a cofactor...etc.), so you have to explicitly call protein_atomgroup.guess_bonds() before protein_mol = plf.Molecule.from_mda(protein_atomgroup)

[cbouy]

Ok I see where the problem is, your protein PDB file contains bond information for only a subset of residues (the non-standard ones like HIE), so the atoms without explicit bonds end up being assigned charges to satisfy valence rules.

You could either try removing the CONECT record at the end of your protein file, or simply forcing bond guessing calculation with:

u = mda.Universe("protein.pdb", guess_bonds=True)
protein_mol = plf.Molecule.from_mda(u)

Or if you have the option, export the protein PDB file with all bonds explicit rather than just the ones for non-standard residues.

Please reopen this issue if you run into other related problems.