Li Zhenyu, Yu Haibo, Zhuang Wei, Mukamel Shaul
Department of Chemistry, University of California, Irvine, CA 92697 USA.
Chem Phys Lett. 2008 Feb 4;452(1-3):78-83. doi: 10.1016/j.cplett.2007.12.022.
Molecular dynamics (MD) simulations are performed for N-methylamide (NMA) in water at 300 K with different force fields. Compared to the three all-atom force fields (CHARMM22, AMBER03, and OPLS-AA), the united-atom force field (GROMOS96) predicts a broader distribution of the peptide OCNH dehedral angle. A map constructed by fitting the npi* and pipi* transition energies as quadratic functions of the NMA geometric variables is used to simulate the excitation energy fluctuations. GROMOS96 predicts blue-shifted npi* and pipi* energies and stronger fluctuations compared to the other three force fields, which indicates that different force fields may predict different spectral lineshapes for proteins.
在300K下，使用不同的力场对水中的N-甲基酰胺（NMA）进行了分子动力学（MD）模拟。与三种全原子力场（CHARMM22、AMBER03和OPLS-AA）相比，联合原子力场（GROMOS96）预测肽OCNH二面角的分布更宽。通过将nπ和ππ跃迁能量拟合为NMA几何变量的二次函数构建的图谱用于模拟激发能波动。与其他三种力场相比，GROMOS96预测nπ和ππ能量发生蓝移且波动更强，这表明不同的力场可能预测蛋白质的不同光谱线形。
