Re: [Open Babel] "complete protonation"

[Pascal M. <pas...@gm...>]

Dear Paul,

> what I want to obtain: Add all possible hydrogens, i.e. every N.3 becomes
> N.4, and every COO- becomes COOH.

Ok - let's use a acid pH of 1, then (option -p1).

> For this purpose, I tried the following things:
> "babel -imol2 b_noH.mol2 -pX -omol2 b_noH_out.mol2"
> X was either 1, 7 or 14
>
> I tried the same for the MOL2 file in which the hydrogens were already in
> place for the non-polar atoms and the neutral nitrogen.
>
> Please find attached the corresponding MOL2 files.

Both files generate the same mol2 file for me:
babel -p1 b_noH.mol2 b_p1.mol2
(b_p1.mol2 attached)
N.4 with 3 H, O.co2 converted in =O (O.2) and OH (O.3).

If it's not the case for you, what's the output of
echo "NCC(=O)O" | babel -i smi -p1 -o smi
?

Check your OpenBabel version (should be 2.3.0) and be sure that there
is only one version installed.

By the way, I always use mol2 files with explicit hydrogens.

Regards,
Pascal