Article ID: 38 - Last Modified: May 4, 2011
In QSite calculations it is common to have a receptor treated with MM and a ligand treated with QM. Can I treat only part of the ligand with QM?
To partition the ligand into a QM and an MM part, you can use hydrogen caps. This is the most flexible partitioning technique. Frozen orbital techniques can only be applied to receptor residues, e.g. Entire Residue and Side Chain cuts.
You can define cuts capped by hydrogen atoms in QSite's QM Settings tab. Select Hydrogen Caps from the Pick menu and then select the QM atom in the workspace, followed by the MM atom on either side to define the cut. Once the hydrogen cap has been created, the Hydrogen cap electrostatics option becomes available and you can choose the electrostatic treatment of MM regions near the cap.
Keywords: QSite, hydrogen caps, ligand, frozen orbital, cut,
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