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

  • Run the following sequence of commands:
obabel in.pdb -O hydrogenated.mol2 -h
grade -in hydrogenated-uniquenames.mol2 -resname TLC
  • Check that the chemistry is right: there are any number of ways to do this, including
  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
  • If the chemistry is wrong, you can use the ccp4i sketcher to fix it
  • N.B. This is the updated procedure as updated Jan 2015. There is now no need to rename hydrogen atoms using hnames.pl with recent versions of grade.

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