Dickson Callum J, Madej Benjamin D, Skjevik Age A, Betz Robin M, Teigen Knut, Gould Ian R, Walker Ross C
Department of Chemistry and Institute of Chemical Biology, Imperial College London , South Kensington SW7 2AZ, United Kingdom.
San Diego Supercomputer Center, University of California San Diego , 9500 Gilman Drive MC0505, La Jolla, California 92093-0505, United States ; Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Drive MC0505, La Jolla, California 92093-0505, United States.
J Chem Theory Comput. 2014 Feb 11;10(2):865-879. doi: 10.1021/ct4010307. Epub 2014 Jan 30.
The AMBER lipid force field has been updated to create Lipid14, allowing tensionless simulation of a number of lipid types with the AMBER MD package. The modular nature of this force field allows numerous combinations of head and tail groups to create different lipid types, enabling the easy insertion of new lipid species. The Lennard-Jones and torsion parameters of both the head and tail groups have been revised and updated partial charges calculated. The force field has been validated by simulating bilayers of six different lipid types for a total of 0.5 μs each without applying a surface tension; with favorable comparison to experiment for properties such as area per lipid, volume per lipid, bilayer thickness, NMR order parameters, scattering data, and lipid lateral diffusion. As the derivation of this force field is consistent with the AMBER development philosophy, Lipid14 is compatible with the AMBER protein, nucleic acid, carbohydrate, and small molecule force fields.
AMBER脂质力场已更新为Lipid14,可使用AMBER分子动力学(MD)软件包对多种脂质类型进行无张力模拟。该力场的模块化特性允许头部和尾部基团进行多种组合以创建不同的脂质类型,从而能够轻松插入新的脂质种类。头部和尾部基团的 Lennard-Jones 势和扭转参数已进行修订,并计算了更新的部分电荷。通过对六种不同脂质类型的双层进行模拟,每种模拟时长总计0.5微秒,且不施加表面张力,对该力场进行了验证;在诸如每个脂质的面积、每个脂质的体积、双层厚度、核磁共振序参数、散射数据和脂质横向扩散等性质方面,与实验结果具有良好的一致性。由于该力场的推导与AMBER的开发理念一致,Lipid14与AMBER蛋白质、核酸、碳水化合物和小分子力场兼容。