Comments (1)
harryjubb
commented on August 18, 2024
Hi Charlotte,
On the web server invocation of Arpeggio, if there are no hydrogens in the input structure, hydrogens are added crudely using OpenBabel's OBMol.AddHydrogens method called correcting for pH 7.4.
The web server doesn't do any minimisation as it's quite computationally intensive, and there's been no testing of the usefulness of the results when running the minimisation with OpenBabel. Hydrogen addition is important but there are better methods, so I've left doing it well outside of the scope of Arpeggio.
I'd recommend adding hydrogens to your input structure before running with Arpeggio with a robust method such as Protoss.
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