molecule protonation state

KNIME Analytics Platform
1

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,

Gio

2

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.

3

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

Simon.

4

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

5

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