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Methodology is discussed for mixed ab initio quantum mechanicsrmolecular mechanics modeling of systems where the quantum Ž . Ž . mechanics QM and molecular mechanics MM regions are within the same molecule. The ab initio QM calculations are at the restricted Hartree]Fock level using the pseudospectral method of the Jaguar program while the MM part is treated with the OPLS force fields implemented in the IMPACT program. The interface between the QM and MM regions, in particular, is elaborated upon, as it is dealt with by ‘‘breaking’’ bonds at the boundaries and using Boys-localized orbitals found from model molecules in place of the bonds. These orbitals are kept frozen during QM calculations. Results from tests of the method to find relative conformational energies and geometries of alanine dipeptides and alanine tetrapeptides are presented along with comparisons to pure QM and pure MM calculations. Q 1999 John Wiley & Sons, Inc. J Comput Chem 20: 1468]1494, 1999

Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide