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openmm / openmmforcefields

CHARMM and AMBER forcefields for OpenMM (with small molecule support)
http://openmm.org
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Best way to protonate ligands / small molecules to get them ready for GAFF #261

Open razvanmarinescu opened 1 year ago

razvanmarinescu commented 1 year ago

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.

mattwthompson commented 1 year ago

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.