Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin.

Autor:	Doemer M; Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland., Maurer P; Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland., Campomanes P; Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland., Tavernelli I; Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland., Rothlisberger U; Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland.
Jazyk:	angličtina
Zdroj:	Journal of chemical theory and computation [J Chem Theory Comput] 2014 Jan 14; Vol. 10 (1), pp. 412-22. Date of Electronic Publication: 2013 Nov 18.
DOI:	10.1021/ct400697n
Abstrakt:	We extended a previously developed force matching approach to systems with covalent QM/MM boundaries and describe its user-friendly implementation in the publicly available software package CPMD. We applied this approach to the challenging case of the retinal protonated Schiff base in dark state bovine rhodopsin. We were able to develop a highly accurate force field that is able to capture subtle structural changes within the chromophore that have a pronounced influence on the optical properties. The optical absorption spectrum calculated from configurations extracted from a MD trajectory using the new force field is in excellent agreement with QM/MM and experimental references.
Databáze:	MEDLINE
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