A QM/MM approach with effective fragment potentials applied to the dipeptide-water structures

An application of the hybrid quantum mechanical and molecular mechanical (QM/MM) model to calculations of the structures of the hydrogen-bonded complex of the dipeptide N-acetyl-L-alanine N'-methylamide with water molecules is described. This particular approach is essentially based on the effective fragment potential theory [J. Phys. Chem. A 105 (2001) 293]. We discuss both options in the QM/MM treatment of the system, considering once the dipeptide as a quantum part and water molecules as a MM subsystem, and vice versa, taking the dipeptide as a collection of effective fragments, while water molecules constitute a QM part. The first method is realized in the GAMESS program, in the second case a new version, combining quantum chemical and molecular mechanical packages is required. Our approach assumes that the MM subsystem is viewed as a flexible composition of effective fragments while fragment- fragment interactions are replaced by the MM force fields. It is shown that these QM/MM models correctly describe the conformational properties of dipeptide, namely, the changes in the backbone angles phi and psi due to complexation with water. (C) 2002 Elsevier Science B.V. All rights reserved.

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