Abstract
RNA molecules are one of the more versatile macromolecules within a cell as they have a variety of structures and functions. Thus, it is important when studying RNA using empirical force fields, to consider the models and methodologies used to study RNA, including the quality of force field parameters. CHARMM27 force field parameters exhibits Watson-Crick (WC) basepair opening in RNA molecules. Here, we present a series of new RNA force field parameters that improve the behavior of RNA molecules. The updates result in changes in the distribution of the 2’-hydroxyl torsion leading to a reduction the frequency and extent of WC base-opening events. As a result of the shift in the 2′-hydroxyl distribution, we observe results that are in improved agreement with experimental and RNA survey data. The optimal force field parameter was applied to study the behavior and folding mechanisms of different types of RNA molecules.
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