Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides

✍ Scribed by Zhi-Xiang Wang; Wei Zhang; Chun Wu; Hongxing Lei; Piotr Cieplak; Yong Duan

• Publisher: John Wiley and Sons
• Year: 2006
• Tongue: English
• Weight: 641 KB
• Volume: 27
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/jcc.20386

✦ Synopsis

Abstract

Based on the AMBER polarizable model (ff02), we have reoptimized the parameters related to the main‐chain (Φ, Ψ) torsion angles by fitting to the Boltzmann‐weighted average quantum mechanical (QM) energies of the important regions (i.e., β, P~II~, α~R~, and α~L~ regions). Following the naming convention of the AMBER force field series, this release will be called ff02pol.rl The force field has been assessed both by energetic comparison against the QM data and by the replica exchange molecular dynamics simulations of short alanine peptides in water. For Ace‐Ala‐Nme, the simulated populations in the β, P~II~ and α~R~ regions were approximately 30, 43, and 26%, respectively. For Ace‐(Ala)~7~‐Nme, the populations in these three regions were approximately 24, 49, and 26%. Both were in qualitative agreement with the NMR and CD experimental conclusions. In comparison with the previous force field, ff02pol.rl demonstrated good balance among these three important regions. The optimized torsion parameters, together with those in ff02, allow us to carry out simulations on proteins and peptides with the consideration of polarization. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 781–790, 2006