This paper provides a set of new force field parameters compatible with the AMBER03 force field to describe five cofactors in the photosystem II of oxygenic photosynthetic organisms: plastoquinone-9, chlorophyll-a, pheophytin-a, heme-b and β-carotene.
In this work, a set of new force field parameters compatible with the AMBER03 force field was presented to describe five cofactors in the photosystem II of oxygenic photosynthetic organisms: plastoquinone-9, chlorophyll-a, pheophytin-a, heme-b and β-carotene. The development of a reliable force field for these cofactors is an essential step for performing Molecular Dynamics simulations of the PSII. In particular, parameters for partial charges, bonds, angles and dihedral-angles were developed with solid theoretical models from quantum mechanics calculations and validations.
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Provides files for performing MD simulation in Gromacs software package: “ffnonboned.itp” includes parameters of the non-bonded interactions; “ffbonded.itp” contains the parameters for bonds, angles and dihedral-angles; “.hdb” file is the hydrogen database, which contains the structural information of how hydrogen atoms are added to the molecules; “.rtp” file contains the partial charges and the structures (bonds, angles, dihedral-angles) of the molecules; All of the atom types appear in the “.rtp” file should have their definitions in the atomtype “.atp” file.
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