CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field

被引:313
作者
Qi, Yifei [1 ,2 ]
Ingolfsson, Helgi I. [3 ,4 ]
Cheng, Xi [1 ,2 ]
Lee, Jumin [1 ,2 ]
Marrink, Siewert J. [3 ,4 ]
Im, Wonpil [1 ,2 ]
机构
[1] Univ Kansas, Dept Mol Biosci, Lawrence, KS 66047 USA
[2] Univ Kansas, Ctr Computat Biol, Lawrence, KS 66047 USA
[3] Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, NL-9747 AG Groningen, Netherlands
[4] Univ Groningen, Zernike Inst Adv Mat, NL-9747 AG Groningen, Netherlands
关键词
MOLECULAR-DYNAMICS SIMULATION; MEMBRANE-BUILDER; PROTEINS; MICELLE; EXTENSION; INSERTION; BILAYERS; MODEL;
D O I
10.1021/acs.jctc.5b00513
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
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.
引用
收藏
页码:4486 / 4494
页数:9
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