Centre de Recherches sur les Macromolécules Végétales, CNRS, BP 53, Grenoble, France.
J Comput Chem. 2011 May;32(7):1400-10. doi: 10.1002/jcc.21726. Epub 2010 Dec 31.
Computer simulations offer a valuable way to study membrane systems, from simple lipid bilayers to large transmembrane protein complexes and lipid-nucleic acid complexes for drug delivery. Their accuracy depends on the quality of the force field parameters used to describe the components of a particular system. We have implemented the widely used CHARMM22 and CHARMM27 force fields in the GROMACS simulation package to (i) combine the CHARMM22 protein force field with two sets of united-atom lipids parameters; (ii) allow comparisons of the lipid CHARMM27 force field with other lipid force fields or lipid-protein force field combinations. Our tests do not show any particular issue with the combination of the all-atom CHARMM22 force field with united-atoms lipid parameters, although pertinent experimental data are lacking to assess the quality of the lipid-protein interactions. The conversion utilities allow automatic generation of GROMACS simulation files with CHARMM nucleic acids and protein parameters and topologies, starting from pdb files using the standard GROMACS pdb2gmx method. CMAP is currently not implemented.
计算机模拟为研究膜系统提供了一种有价值的方法，从简单的脂质双层到用于药物输送的大型跨膜蛋白复合物和脂质-核酸复合物。它们的准确性取决于用于描述特定系统成分的力场参数的质量。我们已经在 GROMACS 模拟包中实现了广泛使用的 CHARMM22 和 CHARMM27 力场，以：(i) 将 CHARMM22 蛋白质力场与两组统一原子脂质参数结合；(ii) 允许比较脂质 CHARMM27 力场与其他脂质力场或脂质-蛋白质力场组合。我们的测试没有显示出与全原子 CHARMM22 力场与统一原子脂质参数结合的任何特殊问题，尽管缺乏相关的实验数据来评估脂质-蛋白质相互作用的质量。转换实用程序允许使用标准 GROMACS pdb2gmx 方法从 pdb 文件自动生成带有 CHARMM 核酸和蛋白质参数和拓扑结构的 GROMACS 模拟文件。CMAP 目前未实现。
