LIPID11: a modular framework for lipid simulations using amber.
LIPID11: a modular framework for lipid simulations using amber.
复制标题
脂质11：使用琥珀色的脂质模拟的模块化框架。
DOI：
10.1021/jp3059992
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发表时间：
2012-09-13
影响因子：
3.3
通讯作者：
Teigen, Knut
中科院分区：
文献类型：
--
作者：
Skjevik, Age A.;Madej, Benjamin D.;Walker, Ross C.;Teigen, Knut
精确模拟复杂的脂双层结构一直是凝聚相分子动力学（MD）的目标。膜结合蛋白的结构和功能高度依赖于脂双层环境，通过实验方法进行研究具有挑战性。在琥珀中，对脂质模拟的关注有限，尽管使用通用琥珀力场（GAFF）取得了一些成功。然而，迄今为止，还没有专门的琥珀色脂质力场。在本文中，我们描述了一种新的电荷衍生策略与琥珀RESP方法相一致的脂质，和一个新的原子和残基命名和类型约定。在第一个实例中，我们结合了这种方法与GAFF参数。其结果是LIPID 11，这是一个灵活的模块化框架，用于模拟脂质，与现有的琥珀力场完全兼容。这里介绍了LIPID 11的电荷推导过程、封顶策略和命名，沿着初步模拟结果和计划的长期参数开发讨论。我们的研究结果表明，Lipid11是一个模块化的框架，磷脂和灵活的起点，为发展一个全面的，琥珀兼容的脂质力场。
Accurate simulation of complex lipid bilayers has long been a goal in condensed phase molecular dynamics (MD). Structure and function of membrane-bound proteins are highly dependent on the lipid bilayer environment and are challenging to study through experimental methods. Within Amber, there has been limited focus on lipid simulations, although some success has been seen with the use of the General Amber Force Field (GAFF). However, to date there are no dedicated Amber lipid force fields. In this paper we describe a new charge derivation strategy for lipids consistent with the Amber RESP approach, and a new atom and residue naming and type convention. In the first instance, we have combined this approach with GAFF parameters. The result is LIPID11, a flexible, modular framework for the simulation of lipids that is fully compatible with the existing Amber force fields. The charge derivation procedure, capping strategy and nomenclature for LIPID11, along with preliminary simulation results and a discussion of the planned long-term parameter development are presented here. Our findings suggest that Lipid11 is a modular framework feasible for phospholipids and a flexible starting point for the development of a comprehensive, Amber-compatible lipid force field.
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影响因子：
5.5
作者：
Goetz, Andreas W.;Williamson, Mark J.;Xu, Dong;Poole, Duncan;Le Grand, Scott;Walker, Ross C.
通讯作者：
Walker, Ross C.
影响因子：
2.4
作者：
Domanski, Jan;Stansfeld, Phillip J.;Beckstein, Oliver
通讯作者：
Beckstein, Oliver
影响因子：
3.4
作者：
Benz, RW;Castro-Román, F;White, SH
通讯作者：
White, SH
DOI：
10.1039/c0cp00111b
发表时间：
2010-07-28
期刊：
Physical chemistry chemical physics : PCCP
影响因子：
--
作者：
Dupradeau FY;Pigache A;Zaffran T;Savineau C;Lelong R;Grivel N;Lelong D;Rosanski W;Cieplak P
通讯作者：
Cieplak P
影响因子：
4.4
作者：
FELLER, SE;ZHANG, YH;BROOKS, BR
通讯作者：
BROOKS, BR