We test a range of standard generalized Born (GB) models and protein force fields for a set of five experimentally characterized, designed peptides comprising alternating blocks of glutamate and lysine, which have been shown to differ significantly in α-helical content. Sixty-five combinations of force fields and GB models are evaluated in >800 μs of molecular dynamics simulations. GB models generally do not reproduce the experimentally observed α-helical content, and none perform well for all five peptides. These results illustrate that these models are not usefully predictive in this context. These peptides provide a useful test set for simulation methods.

中文翻译：

---

广义 Born 隐式溶剂模型不会重现从头设计的 Glu/Lys 肽的二级结构

我们测试了一系列标准广义 Born (GB) 模型和蛋白质力场，用于一组五种经过实验表征的设计肽，包括交替的谷氨酸和赖氨酸块，这些肽已被证明在 α-螺旋含量上有显着差异。在 >800 μs 的分子动力学模拟中评估了力场和 GB 模型的 65 种组合。GB 模型通常不会重现实验观察到的 α-螺旋含量，并且所有五种肽都没有表现良好。这些结果表明，这些模型在这种情况下没有有用的预测性。这些肽为模拟方法提供了有用的测试集。