How do I include a metal ion in a QSite calculation?

First prepare the protein with the Protein Preparation Wizard. For older releases, you should use the Treat Metals option. (If you do not treat the metal, you must delete any bonds to the metal and use the Atom Properties tab of the Build panel to enter the correct formal charge and PDB atom name.) Then add the ion to the QM region, and verify that the charge and multiplicity values listed in the QM Settings tab are valid for the entire defined QM region.

For more information on protein preparation, see the Protein Preparation Guide.

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