In the Protein Preparation Wizard, what exactly are the "treat metals" and "metal mode" options?

"Treat metals" (Suite 2009) or "Create zero-order bonds to metals (Suite 2010 on) replaces covalent bonds to metals with zero-order (dashed) bonds, and adjusts the formal charges of the metal and ligating atoms accordingly. The zero-order bonds help constrain the coordination geometry during subsequent calculations, and they also allow formal charges to be distributed across the coordination group. Force fields do not generally have terms for covalent bonding to metals, so they must be treated as ionic.

"Metal mode" (Suite 2009) or "Metal binding states" (Suite 2010 on) is an option for generating het states that instructs Epik to return additional ligand states that are suitable for metal binding, but would have high state penalties in the absence of such an interaction. If your active site has a metal, we suggest using this option. Similarly, if you'll be docking ligands to a metal and want to apply Epik state penalties to the docking scores, you should use the "Add metal binding states" Epik option when preparing your ligands with LigPrep.

Keywords: treat metals, metal mode, generate het states, metal binding, Maestro

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