Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions.

ABSTRACT: Molecular dynamics (MD) simulations became a leading tool for investigation of structural dynamics of nucleic acids. Despite recent efforts to improve the empirical potentials (force fields, ffs), RNA ffs have persisting deficiencies, which hamper their utilization in quantitatively accurate simulations. Previous studies have shown that at least two salient problems contribute to difficulties in the description of free-energy landscapes of small RNA motifs: (i) excessive stabilization of the unfolded single-stranded RNA ensemble by intramolecular base-phosphate and sugar-phosphate interactions and (ii) destabilization of the native folded state by underestimation of stability of base pairing. Here, we introduce a general ff term (gHBfix) that can selectively fine-tune nonbonding interactio

SUBMITTER: Kuhrova P 

PROVIDER: S-EPMC7491206 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature