openmm
Best way to protonate ligands / small molecules to get them ready for GAFF
What is the best way to protonate a ligand / small molecule?
I think I successfully managed to protonate my 58H ligand with pdb4amber (using the --add-hydrogens option) and I checked the file afterwards, and it seemed to have added all 26 hydrogens on my ligand (as much as there are shown on ligand-expo: http://ligand-expo.rcsb.org/reports/5/58H/)
But @jchodera, you suggested that I actually download that structure instead, and align it to my system. Is this better than protonating it myself? It complicates my workflow a bit, but if this is better I can switch to this strategy.
You may have better luck figuring out recommended GAFF usage via one of the Amber mailing lists. I personally don't know what these preparation pipelines assume so I can't help much.
Closing this issue since it is over a year old with no additional response, and it doesn't appear to involve an outstanding problem. This issue can be reopened if needed.
