Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin
Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin
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DOI：
10.1021/ct400697n
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发表时间：
2014-01-01
影响因子：
5.5
通讯作者：
Rothlisberger, Ursula
中科院分区：
文献类型：
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作者：
Doemer, Manuel;Maurer, Patrick;Rothlisberger, Ursula
我们扩展了以前开发的力匹配方法与共价QM/MM边界系统，并描述其用户友好的实现在公开可用的软件包CPMD。我们将这种方法应用于具有挑战性的情况下，视网膜质子化的席夫碱在黑暗状态下的牛视紫红质。我们能够开发出一种高度精确的力场，能够捕捉到发色团内部的细微结构变化，这些变化对光学性质有显著影响。从MD轨迹提取的配置使用新的力场计算的光学吸收光谱与QM/MM和实验参考非常一致。
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.