CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field
CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field
复制标题
DOI：
10.1021/acs.jctc.5b00513
复制
发表时间：
2015-09-01
影响因子：
5.5
通讯作者：
Im, Wonpil
中科院分区：
文献类型：
--
作者：
Qi, Yifei;Ingolfsson, Helgi I.;Im, Wonpil
粗粒度模拟被广泛用于研究大型生物系统。尽管如此，构建这样的模拟系统变得非常重要，特别是当涉及到各种脂质类型的膜时。利用全原子CHARMM-GUI模块中的框架，我们开发了CHARMM-GUI Martini Maker，用于使用Martini力场构建溶液，胶束，双层和囊泡系统以及随机分布的脂质系统。Martini Maker支持82种脂质类型和不同口味的Martini力场，包括极性和非极性Martini，干Martini和ElNeDyn（蛋白质的弹性网络模型）。Martini Maker生成的系统的质量通过模拟各种涉及蛋白质和脂质的例子得到验证。我们希望Martini Maker能够成为一个有用的工具，以一种用户友好的方式对大型复杂的生物分子系统进行建模。
Coarse-grained simulations are widely used to study large biological systems. Nonetheless, building such simulation systems becomes nontrivial, especially when membranes with various lipid types are involved. Taking advantage of the frameworks in all-atom CHARMM-GUI modules, we have developed CHARMM-GUI Martini Maker for building solution, micelle, bilayer, and vesicle systems as well as systems with randomly distributed lipids using the Martini force field. Martini Maker supports 82 lipid types and different flavors of the Martini force field, including polar and nonpolar Martini, Dry Martini, and ElNeDyn (an elastic network model for proteins). The qualities of the systems generated by Martini Maker are validated by simulations of various examples involving proteins and lipids. We expect Martini Maker to be a useful tool for modeling large, complicated biomolecular systems in a user-friendly way.