molecule protonation state

Hi guys,

Do you know if there is a free, opensource node to treat protonation state of molecules? (e.g. neutralize molecules, protonate them at neutral pH, calculate their pKa, calculate their formal charge, etc.)

Thanks in advance,


Hi Gio,

I'm afraid there is no such node or even program. Openbabel pretends to do such thing:

-p <pH> Add hydrogens appropriate for pH (use transforms in phmodel.txt)

but it didn't seem to work, at least for me.

I know the MOE nodes can do this in KNIME, but these arent free I'm afraid.


Also Schrodinger (Epik) and ChemAxon commercial nodes (I think) has this feature.

OK guys, anyway thank you so much for the explanation!