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Geometry and Excitation Energy Fluctuations of NMA in Aqueous Solution with CHARMM, AMBER, OPLS, and GROMOS Force Fields: Implications for Protein Ultraviolet Spectra Simulation.

ABSTRACT: 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.

SUBMITTER: Li Z 

PROVIDER: S-EPMC2344158 | biostudies-literature | 2008 Feb

REPOSITORIES: biostudies-literature

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Geometry and Excitation Energy Fluctuations of NMA in Aqueous Solution with CHARMM, AMBER, OPLS, and GROMOS Force Fields: Implications for Protein Ultraviolet Spectra Simulation.

Li Zhenyu Z   Yu Haibo H   Zhuang Wei W   Mukamel Shaul S  

Chemical physics letters 20080201 1-3

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 predict  ...[more]

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