Through extensive simulation of RNA motifs we have exposed and overcome issues with the AMBER force fields for nucleic acids. Motifs include a wide variety of small RNA structures determined by NMR, a large series of DNA duplexes and quadruplexes, and also most of the RNA tetraloop structures. To improve the force fields, high level QM simulations, both in-vacuo and in implicit solvent, have been performed on all of the RNA dinucleotides and mono-nucleotides in a variety of conformations. In addition, extensive sampling of small RNA nucleotides have been performed for further assessment and validation. To faciliate dissemination of the results and management and analysis of the data, we have also explored automated solutions to annodate and display the data and also to improve detailed analysis of the time-dependence and convergence of many derived properties from the simulation.

Assessing, validating, and developing AMBER force fields for RNA

245th National Meeting (2013)

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