Re: [Open Babel] "complete protonation"

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

Dear Paul,

> how do I enable a "complete protonation" of all atoms within PyBEL?

Do you mean ionization?

>  A small
> test of the OpenBabel Windows version revealed that COO- is converted COOH,
> but R-NH2 is not converted to R-NH3+.
> As data source, I work with MOL2 files, and this shall be the output as
> well.
> For the last group, the original atom type is set to N.3, and it is not
> changed to N.4, although I chose a high pH of 14 to "protonate" the
> molecule.

Try a pH around 7 if you want both COO- and NH3+. In basic condition,
amines are not protonated.

echo "NCC(=O)O" | babel -i smi -p1 -o smi
[NH3+]CC(=O)O
(N.4 if mol2 outpout)

echo "NCC(=O)O" | babel -i smi -p7 -o smi
[NH3+]CC(=O)[O-]

echo "NCC(=O)O" | babel -i smi -p14 -o smi
NCC(=O)[O-]

Regards,
Pascal