When using QSite can I make a cut inside a ligand rather than putting the whole ligand inside the QM region ?

Yes, but to make intra-molecular cuts in entities that are non-standard residues you should use the hydrogen capping technique to separate the QM and MM regions. When doing this please remember that if you have an MM receptor and a ligand that the energies and interactions of the MM part of the ligand will be indistinguishable from, for example, that of the the MM receptor or MM water molecules.

Keywords: Hydrogen caps, ligand, energy terms, cuts

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