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Computational methods for the study of enzymic reaction mechanisms III: a perturbation plus QM/MM approach for calculating relative free energies of protonation

Cummins, Peter; Gready, Jill


We describe a coupling parameter, that is, perturbation, approach to effectively create and annihilate atoms in the quantum mechanical Hamiltonian within the closed shell restricted Hartree-Fock formalism. This perturbed quantum mechanical atom (PQA) method is combined with molecular mechanics (MM) methods (PQA/MM) within a molecular dynamics simulation, to model the protein environment (MM region) effects that also make a contribution to the overall free energy change. Using the semiempirical...[Show more]

CollectionsANU Research Publications
Date published: 2005
Type: Journal article
Source: Journal of Computational Chemistry
DOI: 10.1002/jcc.20192


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