NDLI: Large-Scale QM/MM Calculations of Electronic Excitations in Yellow Protein: Toward Petascale Level of Protein Calculations

Content Provider	IEEE Xplore Digital Library
Author	Freindorf, M. Jones, M.D. Yihan Shao Jing Kong Furlani, T.R.
Copyright Year	2007
Description	Author affiliation: State Univ. of New York at Buffalo, Buffalo (Freindorf, M.; Jones, M.D.)
Abstract	Large-scale combined quantum mechanical -molecular mechanical (QM/MM) calculations of an active-site of the photoactive yellow protein have been performed. The calculations are based on a 10 ns molecular dynamics simulation of the protein, and a 10 ns molecular dynamics of the protein chromophor in water solution, using AMBER force fields. For each of these simulations, 1,000 randomly chosen configurations were selected and individual combined QM/MM calculations for each configuration were performed. The QM/MM calculations included geometry optimization of the protein chromophor calculated at the AMBER/B3LYP/6 -31+ G* level of theory, and electronic-excitation calculations performed at the AMBER/TDDFT/B3LYP/aug-cc-pVTZ level of theory. Final results are reported as averaged data based on an ensemble of 1,000 structures obtained from the molecular dynamics simulations. The results of the calculations are compared with experimental data of electronic excitations of the protein photoreceptor in the protein, in water solution and in the gas phase.
Starting Page	614
Ending Page	619
File Size	3321241
Page Count	6
File Format	PDF
ISBN	9781424415090
DOI	10.1109/BIBE.2007.4375624
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2007-10-14
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Large-scale systems Photoreceptors Absorption Quantum computing Quantum mechanics Solvents Petascale computing Solid modeling Geometry
Content Type	Text
Resource Type	Article

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