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)

The procedure

obabel in.pdb -O hydrogenated.mol2 -h
grade -in hydrogenated-uniquenames.mol2 -resname TLC
  1. look at the structure (coot -p grade_TLC.pdb) and check that it looks right
  2. run obprop grade_TLC.pdb and check that the SMILES string corresponds to the one you have in your records
  3. run obabel hydrogenated-uniquenames.mol2 img.svg -d and check in your favorite SVG viewer (firefox is the easiest one to get hold of) that the diagram is right

Any questions regarding our software or this wiki should be directed to buster-develop@globalphasing.com