I have some PDB structures of small molecules with missing hydrogens. Is there a software available that places missing hydrogens and assigns a charge to the molecule that is reliable? I am looking for an automatic tool that returns a PDB with added Hydrogens and the overall charge (I can do some programming if I need to combine output from multiple programs to accomplish this or something.)
It is enough for me if you suggest a couple of FREE tools (I don't have resources to buy a commercial license, but I am academic, in case they offer free academic licenses), with associated papers that evaluate their performance that I can cite. For example, a free tool that calculates pKa values of ionizable groups would solve my problem, if you can also suggest a tool that automatically detects ionizable groups in molecules.
I have used Avogadro to add hydrogens (though I don't know how to compute the charge with it), but I've found that some hydrogens aren't well placed. Is there a better tool available for this task?