Abstract
We developed new parameters for molecular dynamics (MD) simulations, namely partial atomic charges, equilibrium bond-lengths, angles, dihedrals, atom types, and force constants of chlorophyll a (Chl) and plastoquinone (PQ), and both reduced and neutral form of primary acceptor (PHO) molecule. These parameters are essential for MD simulations that can interpret various structure functional relationships during primary processes of charge separation and stabilization in photosystem 2 reaction centres.
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Palencar, P., Vacha, F. & Kuty, M. Force field development on pigments of photosystem 2 reaction centre. Photosynthetica 43, 417–420 (2005). https://doi.org/10.1007/s11099-005-0066-2
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DOI: https://doi.org/10.1007/s11099-005-0066-2