Development of polarizable models for molecular mechanical calculations II: induced dipole models significantly improve accuracy of intermolecular interaction energies.
Development of polarizable models for molecular mechanical calculations II: induced dipole models significantly improve accuracy of intermolecular interaction energies.
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DOI：
10.1021/jp1121382
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发表时间：
2011-03-31
影响因子：
3.3
通讯作者：
Duan, Yong
中科院分区：
文献类型：
--
作者：
Wang, Junmei;Cieplak, Piotr;Li, Jie;Wang, Jun;Cai, Qin;Hsieh, MengJuei;Lei, Hongxing;Luo, Ray;Duan, Yong
在配套文件中，我们提出了一套诱导偶极相互作用模型使用四种类型的屏蔽函数，其中包括Applequist（无屏蔽），Thole线性，Thole指数模型，和Thole Tinker-like（另一种形式的指数屏蔽函数）功能。在这项工作中，我们使用大量的氨基酸类似物对，经常观察到的蛋白质结构作为基准评估极化率模型的性能。在MP2/aug-cc-pVTZ//MP2/6 - 311 ++ G（d，p）水平下，采用基组叠加误差（BSSE）修正，计算了每个氨基酸对的量子力学相互作用能，并与分子力学结果进行了比较。令人鼓舞的是，所有可极化模型在再现BSSE校正的量子力学相互作用能方面都明显优于加性F94和F03模型（分别模拟AMBER ff94/ff99和ff03力场）。特别地，对于模型AL（Thole线性）、模型AE（Thole指数）和模型AT（Thole Tinker-like），集合A（其中1 - 2和1 - 3相互作用被关闭并且包括所有1 - 4相互作用）中的三个Thole模型的均方根误差（RMSE）分别为1.456、1.417和1.406 kcal/mol。相比之下，F94和F03模型的RMSE分别为3.729和3.433 kcal/mol。平均无符号误差（AUE）也观察到类似的趋势，AL、AE、AT、F94/ff99和F03的AUE分别为1.057、1.025、1.011、2.219和2.070 kcal/mol。基于趋势线斜率的分析表明，两种固定电荷模型分别大幅低估了非电荷-电荷相互作用的相对强度24%（F03）和35%（F94），而四种可极化模型分别高估了5%（AT）、3%（AL、AE）和13%（AA）的相对强度。通过调整货车德瓦耳斯参数进一步提高了一致性。与固定电荷模型相比，从显着提高的精度来看，可极化模型有望成为开发高质量可极化力场用于蛋白质和核酸模拟的基础。
In the companion paper, we presented a set of induced dipole interaction models using four types of screening functions, which include the Applequist (no screening), the Thole linear, the Thole exponential model, and the Thole Tinker-like (another form of exponential screening function) functions. In this work, we evaluate the performance of polarizability models using large set of amino acid analog pairs that are frequently observed in protein structures as a benchmark. For each amino acid pair we calculated quantum mechanical interaction energies at the MP2/aug-cc-pVTZ//MP2/6-311++G(d,p) level with the basis set superposition error (BSSE) correction and compared them with molecular mechanics results. Encouragingly, all the polarizable models significantly outperform the additive F94 and F03 models (mimicking AMBER ff94/ff99 and ff03 force fields, respectively) in reproducing the BSSE-corrected quantum mechanical interaction energies. Particularly, the root-mean-square errors (RMSE) for three Thole models in Set A (where the 1–2 and 1–3 interactions are turned off and all 1–4 interactions are included) are 1.456, 1.417 and 1.406 kcal/mol for Model AL (Thole Linear), Model AE (Thole exponential) and Model AT (Thole Tinker-like), respectively. In contrast, the RMSE are 3.729 and 3.433 kcal/mol for F94 and F03 models, respectively. A similar trend was observed for the average unsigned errors (AUE), which are 1.057, 1.025, 1.011, 2.219 and 2.070 kcal/mol for AL, AE, AT, F94/ff99 and F03, respectively. Analyses based on the trend line slopes indicate that the two fixed charge models substantially underestimate the relative strengths of non-charge-charge interactions by 24% (F03) and 35% (F94), respectively, whereas the four polarizable models over-estimate the relative strengths by 5% (AT), 3% (AL, AE) and 13% (AA), respectively. Agreement was further improved by adjusting the van der Waals parameters. Judging from the notably improved accuracy in comparison to the fixed charge models, the polarizable models are expected to form the foundation for the development of high quality polarizable force fields for protein and nucleic acid simulations.
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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：
5.6
作者：
LEVITT, M;PERUTZ, MF
通讯作者：
PERUTZ, MF
影响因子：
3
作者：
Duan, Y;Wu, C;Kollman, P
通讯作者：
Kollman, P
影响因子：
3
作者：
Cieplak, P;Caldwell, J;Kollman, P
通讯作者：
Kollman, P
影响因子：
15
作者：
APPLEQUIST, J;CARL, JR;FUNG, KK
通讯作者：
FUNG, KK