Development of Accurate Force Fields for Mg<sup>2+</sup> and Triphosphate\nInteractions in ATP·Mg<sup>2+</sup> and GTP·Mg<sup>2+</sup> Complexes

In\ncells, adenosine triphosphate (ATP) and guanosine triphosphate\n(GTP) molecules typically form tricoordinated or bicoordinated ATP·Mg<sup>2+</sup> or GTP·Mg<sup>2+</sup> complexes with Mg<sup>2+</sup> ions and bind to proteins, participating in and regulating many\nimportant cellular functions. The accuracy of their force field parameters\nplays a crucial role in studying the function-related conformations\nof ATP·Mg<sup>2+</sup> or GTP·Mg<sup>2+</sup> using molecular\ndynamics (MD) simulations. The parameters developed based on the methyl\ntriphosphate model in existing AMBER force fields cannot accurately\ndescribe the conformational distribution of tricoordinated or bicoordinated\nATP·Mg<sup>2+</sup> or GTP·Mg<sup>2+</sup> complexes in\nsolution. In this study, we develop force field parameters for the\ntriphosphate group based on the new ribosyl triphosphate model, considering\nthe dihedral coupling effect, accurate van der Waals (vdW) interactions,\nand the influence of strongly polarized charges on conformational\nbalance. The new force fields can accurately describe the conformational\nbalance of tricoordinated and bicoordinated ATP·Mg<sup>2+</sup> or GTP·Mg<sup>2+</sup> conformations in solution and can be\napplied to simulate biological systems containing ATP·Mg<sup>2+</sup> or GTP·Mg<sup>2+</sup> complexes.