Geometry and excitation energy fluctuations of NMA in aqueous solution with CHARMM, AMBER, OPLS, and GROMOS force fields: Implications for protein ultraviolet spectra simulation

Authors

Zhenyu Li, University of California-Irvine
Haibo Yu, University of WollongongFollow
Wei Zhuang, University of California-Irvine
Shaul Mukamel, University of California-Irvine

RIS ID

38764

Publication Details

Li, Z., Yu, H., Zhuang, W. & Mukamel, S. (2008). Geometry and excitation energy fluctuations of NMA in aqueous solution with CHARMM, AMBER, OPLS, and GROMOS force fields: Implications for protein ultraviolet spectra simulation. Chemical Physics Letters, 452 78-83.

Abstract

Molecular dynamics (MD) simulations are performed for N-methylacetamide (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) pre- dicts a broader distribution of the peptide OCNH dehedral angle. A map constructed by fitting the np� and pp� transition energies as quadratic functions of the NMA geometric variables is used to simulate the excitation energy fluctuations. GROMOS96 predicts blue shifted np� and pp� energies and stronger fluctuations compared to the other three force fields, which indicates that different force fields may predict different spectral lineshapes for proteins.