The generalized hybrid orbital method for combined quantum mechanical/molecular mechanical calculations: formulation and tests of the analytical derivatives |
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Authors: | Patricia Amara Martin J Field Cristobal Alhambra Jiali Gao |
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Institution: | (1) Institut de Biologie Structurale – Jean-Pierre Ebel, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France, FR;(2) Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260, USA, US |
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Abstract: | Hybrid quantum mechanical (QM) and molecular mechanical (MM) potentials are becoming increasingly important for studying
condensed-phase systems but one of the outstanding problems in the field has been how to treat covalent bonds between atoms
of the QM and MM regions. Recently, we presented a generalized hybrid orbital (GHO) method that was designed to tackle this
problem for hybrid potentials using semiempirical QM methods Gao et al. (1998) J Phys Chem A 102: 4714–4721]. We tested the method on some small molecules and showed that it performed well when compared to the purely
QM or MM potentials. In this article, we describe the formalism for the determination of the GHO energy derivatives and then
present the results of more tests aimed at validating the model. These tests, involving the calculation of the proton affinities
of some model compounds and a molecular dynamics simulation of a protein, indicate that the GHO method will prove useful for
the application of hybrid potentials to solution-phase macromolecular systems.
Received: 4 October 1999 / Accepted: 18 December 1999 / Published online: 5 June 2000 |
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Keywords: | : Hybrid method Analytic first derivatives Geometry optimization Molecular dynamics Protein simulation |
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