This may be more of a question than an issue or bug.
I ran PROPKA3 on the whole C. elegans alphafold proteome (~19000 .pdbs) and see no backbone h-bonding deltas for Lysine. Briefly checking for arginine in a few files I see none, also. I see plenty for His and acidic residues.
Is there a chemistry reason for this, or a peculiarity of this dataset or the PROPKA algorithm?
I've only been interested in sidechain pKas for a few days, so I apologise in advance if this is a silly question.
This may be more of a question than an issue or bug.
I ran PROPKA3 on the whole C. elegans alphafold proteome (~19000 .pdbs) and see no backbone h-bonding deltas for Lysine. Briefly checking for arginine in a few files I see none, also. I see plenty for His and acidic residues.
Is there a chemistry reason for this, or a peculiarity of this dataset or the PROPKA algorithm?
I've only been interested in sidechain pKas for a few days, so I apologise in advance if this is a silly question.