GLYCAM06 is a generalisable biomolecular force field that is extendible to diverse molecular classes in the spirit of a small-molecule force field. Here we report parameters for lipids, lipid bilayers and glycolipids for use with GLYCAM06. Only three lipid-specific atom types have been introduced, in keeping with the general philosophy of transferable parameter development. Bond stretching, angle bending, and torsional force constants were derived by fitting to quantum mechanical data for a collection of minimal molecular fragments and related small molecules. Partial atomic charges were computed by fitting to ensemble-averaged quantum-computed molecular electrostatic potentials. In addition to reproducing quantum mechanical internal rotational energies and experimental valence geometries for an array of small molecules, condensed-phase simulations employing the new parameters are shown to reproduce the bulk physical properties of a DMPC lipid bilayer. The new parameters allow for molecular dynamics simulations of complex systems containing lipids, lipid bilayers, glycolipids, and carbohydrates, using an internally consistent force field. By combining the AMBER parameters for proteins with the GLYCAM06 parameters, it is also possible to simulate protein–lipid complexes and proteins in biologically relevant membrane-like environments.

中文翻译：

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将 GLYCAM06 生物分子力场扩展到脂质、脂质双层和糖脂

GLYCAM06 是一种可推广的生物分子力场，本着小分子力场的精神，可扩展到不同的分子类别。在这里，我们报告了与 GLYCAM06 一起使用的脂质、脂质双层和糖脂的参数。根据可转移参数开发的一般理念，仅引入了三种脂质特定的原子类型。键拉伸、角度弯曲和扭力常数是通过拟合量子力学数据得出的，用于收集最小分子碎片和相关小分子。通过拟合整体平均量子计算分子静电势来计算部分原子电荷。除了为一系列小分子再现量子力学内部旋转能和实验价几何之外，显示使用新参数的凝聚相模拟重现了 DMPC 脂质双层的整体物理特性。新参数允许使用内部一致的力场对包含脂质、脂质双层、糖脂和碳水化合物的复杂系统进行分子动力学模拟。通过将蛋白质的 AMBER 参数与 GLYCAM06 参数相结合，还可以在生物相关的类似膜的环境中模拟蛋白质-脂质复合物和蛋白质。