Re: [Open Babel] add hydrogens appropriate for pH

[Geoffrey H. <geo...@gm...>]

> No matter how acid I set the pH aniline (pKa 4.6) is never protonated

It's not a general model of pH-dependent protonation. It has a set of rules, particularly for amino acids.

For more accurate pKa determination, you'll probably want semiempirical quantum calculations or a more complete model. Several people have suggested interest and I've given them some pointers, but no contributions yet. (It's not trivial.)

-Geoff