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用于与液体模拟全原子力场的优化势相结合的联合原子脂质参数。

United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field.

作者信息

Ulmschneider Jakob P, Ulmschneider Martin B

机构信息

IWR, University of Heidelberg, Heidelberg, Germany, and Department of Chemistry, University of Utrecht, Utrecht, The Netherlands.

出版信息

J Chem Theory Comput. 2009 Jul 14;5(7):1803-13. doi: 10.1021/ct900086b.

Abstract

We have developed a new united-atom set of lipid force field parameters for dipalmitoylphosphatidylcholine (DPPC) lipid bilayers that can be combined with the all-atom optimized potentials for liquid simulations (OPLS-AA) protein force field. For this, all torsions have been refitted for a nonbonded 1-4 scale factor of 0.5, which is the standard in OPLS-AA. Improved van der Waals parameters have been obtained for the acyl lipid tails by matching simulation results of bulk pentadecane against recently improved experimental measurements. The charge set has been adjusted from previous lipid force fields to allow for an identical treatment of the alkoxy ester groups. This reduces the amount of parameters required for the model. Simulation of DPPC bilayers in the tension-free NPT ensemble at 50 °C gives the correct area per lipid of 62.9 ± 0.1 Å(2), which compares well with the recently refined experimental value of 63.0 Å(2). Electron density profiles and deuterium order parameters are similarly well reproduced. The new parameters will allow for improved simulation results in microsecond scale peptide partitioning simulations, which have proved problematic with prior parametrizations.

摘要

我们已经为二棕榈酰磷脂酰胆碱(DPPC)脂质双层开发了一套新的联合原子脂质力场参数,该参数可与用于液体模拟的全原子优化势(OPLS-AA)蛋白质力场相结合。为此,所有扭转角都针对非键合1-4比例因子0.5进行了重新拟合,这是OPLS-AA中的标准值。通过将本体十五烷的模拟结果与最近改进的实验测量值进行匹配,获得了改进的酰基脂质尾部范德华参数。电荷集已根据先前的脂质力场进行了调整,以便对烷氧基酯基团进行相同的处理。这减少了模型所需的参数数量。在50°C的无张力NPT系综中对DPPC双层进行模拟,得到每个脂质正确的面积为62.9±0.1 Ų,这与最近细化的实验值63.0 Ų相当。电子密度分布和氘序参数同样得到了很好的再现。新参数将在微秒级肽分配模拟中产生改进的模拟结果,而先前的参数化在这方面已被证明存在问题。

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