Current status of the AMOEBA polarizable force field.
Current status of the AMOEBA polarizable force field.
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DOI：
10.1021/jp910674d
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发表时间：
2010-03-04
期刊：
影响因子：
--
通讯作者：
Head-Gordon T
中科院分区：
文献类型：
--
作者：
Ponder JW;Wu C;Ren P;Pande VS;Chodera JD;Schnieders MJ;Haque I;Mobley DL;Lambrecht DS;DiStasio RA Jr;Head-Gordon M;Clark GN;Johnson ME;Head-Gordon T
在过去的几年里，分子力场已经接近了一个世代的过渡，从完善的和良好的调整，但本质上是有限的，定点电荷模型转向更复杂和昂贵的极化模型，应该允许更准确的描述分子特性。最近推出的AMOEBA力场是下一代理论模型的一个领先的公开例子，但迄今为止只得到了相对有限的验证，我们在这里解决。我们表明，AMOEBA力场实际上是一个显着的改进，特别是小分子结构和热力学观测的固定电荷模型，虽然进一步微调是必要的，以描述溶剂化自由能的药物样小分子，远离环境条件下的动力学特性，并可能改善芳香族相互作用。最先进的电子结构计算显示，一般非常好的协议与AMOEBA要求的问题，如相对构象能的丙氨酸四肽和异构体的水硫酸盐复合物。AMOEBA在蛋白质-配体结合和计算X射线晶体学方面特别成功，其中极化和精确的静电是关键。
Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models towards more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with AMOEBA for demanding problems such as relative conformational energies of the alanine tetrapeptide and isomers of water sulfate complexes. AMOEBA is shown to be especially successful on protein-ligand binding and computational X-ray crystallography where polarization and accurate electrostatics are critical.
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影响因子：
4.1
作者：
BENNETT, CH
通讯作者：
BENNETT, CH
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：
Duan, Y;Wu, C;Kollman, P
通讯作者：
Kollman, P
影响因子：
4.4
作者：
ESSMANN, U;PERERA, L;PEDERSEN, LG
通讯作者：
PEDERSEN, LG
影响因子：
3.3
作者：
Boresch, S;Tettinger, F;Karplus, M
通讯作者：
Karplus, M