Transferability of the Electrostatic Parameters of the Polarizable Gaussian Multipole Model.
Transferability of the Electrostatic Parameters of the Polarizable Gaussian Multipole Model.
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DOI：
10.1021/acs.jctc.2c01048
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发表时间：
2023-02-14
影响因子：
5.5
通讯作者：
Luo, Ray
中科院分区：
文献类型：
--
作者：
Zhao, Shiji;Cieplak, Piotr;Duan, Yong;Luo, Ray
精确度和可转移性是分子机械力场的两个非常理想的性质。与广泛使用的以原子为中心的固定点部分电荷来模拟静电相互作用的点电荷附加力场相比，极化力场在模拟原子极化效应方面具有优势。前人的工作已经证明了最近发展的可极化高斯多极(PGM)模型的准确性。在这项工作中，我们评估了有(PGM-PERM)和没有(PGM-IND)原子永久偶极子的PGM模型的静电参数的可传递性，通过再现没有静电参数的分子/低聚物周围的静电势。令人鼓舞的是，在以下测试中，PGM-PERM和PGM-IND模型都显示出比加法模型显著提高的可转移性：(1)从水单体到水低聚物簇；(2)跨不同构象的氨基酸二肽和四肽；(3)从氨基酸四肽到较长的多肽；以及(4)从碱基单体到Watson-Crick碱基对二聚体和四聚体。此外，我们还证明了在α-IND和β-PERM模型中，利用氨基酸四肽在PGM-IND和PGM-PERM构象中的双构象拟合不仅可以在不同的四肽构象之间进行转移，而且可以从四肽到长度从1到20个重复残基的多肽。此外，观察到PGM-ind模型比点电荷相加模型具有明显更好的准确性和可转移性，尽管它们具有相同的参数数量，这强烈地表明了分子内极化效应的重要性。总之，这项工作和以前的工作一起表明，PGM模型具有准确性和可转移性，有望成为开发下一代可极化力场的基础，用于模拟各种极化敏感的生物系统和过程。
Accuracy and transferability are the two highly desirable properties of molecular mechanical force fields. Compared with the extensively used point-charge additive force fields that apply fixed atom-centered point partial charges to model electrostatic interactions, polarizable force fields are thought to have the advantage of modeling the atomic polarization effects. Previous works have demonstrated the accuracy of the recently developed polarizable Gaussian multipole (pGM) models. In this work, we assessed the transferability of the electrostatic parameters of the pGM models with (pGM-perm) and without (pGM-ind) atomic permanent dipoles in terms of reproducing the electrostatic potentials surrounding molecules/oligomers absent from electrostatic parameterizations. Encouragingly, both the pGM-perm and pGM-ind models show significantly improved transferability than the additive model in the tests (1) from water monomer to water oligomer clusters; (2) across different conformations of amino acid dipeptides and tetrapeptides; (3) from amino acid tetrapeptides to longer polypeptides; and (4) from nucleobase monomers to Watson–Crick base pair dimers and tetramers. Furthermore, we demonstrated that the double-conformation fittings using amino acid tetrapeptides in the αR and β conformations can result in good transferability not only across different tetrapeptide conformations but also from tetrapeptides to polypeptides with lengths ranging from 1 to 20 repetitive residues for both the pGM-ind and pGM-perm models. In addition, the observation that the pGM-ind model has significantly better accuracy and transferability than the point-charge additive model, even though they have an identical number of parameters, strongly suggest the importance of intramolecular polarization effects. In summary, this and previous works together show that the pGM models possess both accuracy and transferability, which are expected to serve as foundations for the development of next-generation polarizable force fields for modeling various polarization-sensitive biological systems and processes.
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影响因子：
6.1
作者：
CONNOLLY, ML
通讯作者：
CONNOLLY, ML
DOI：
10.1088/0953-8984/21/33/333102
发表时间：
2009-08-19
期刊：
Journal of physics. Condensed matter : an Institute of Physics journal
影响因子：
--
作者：
Cieplak P;Dupradeau FY;Duan Y;Wang J
通讯作者：
Wang J
影响因子：
3
作者：
COX, SR;WILLIAMS, DE
通讯作者：
WILLIAMS, DE
影响因子：
3
作者：
CHIRLIAN, LE;FRANCL, MM
通讯作者：
FRANCL, MM
影响因子：
3
作者：
Cieplak, P;Caldwell, J;Kollman, P
通讯作者：
Kollman, P