We would generally strongly recommend against using PDB files without hydrogen atoms as the sole source of information about the chemical state of a compound.
However, there are situations, most obviously working from files deposited without hydrogens in corporate databases (if you're working with actual PDB entries you should use grade_PDB_ligand which takes advantage of the carefully-curated wwPDB compound database), where that's all you've got in electronic format, but you might have a diagram or a SMILES string available to check the results.
To convert a PDB file without hydrogens into a mol2 file usable by grade, you will need a reasonably modern version of openbabel (2.3.0 is what we've tested with)
obabel in.pdb -O hydrogenated.mol2 -h grade -in hydrogenated-uniquenames.mol2 -resname TLC
Any questions regarding our software or this wiki should be directed to buster-develop@globalphasing.com