Tom Cheatham
Affiliation
University of Utah, USA - Cheatham Group
Over 30 years of RNA simulation - lessons learned, force fields, modified nucleotides and salt.
Abstract
Starting with the Cornell et al. “ff94” force field and the implementation and parallelization of the particle mesh Ewald method, the first papers from my PhD with Peter Kollman demonstrated stable simulations of DNA, RNA, and proteins, investigated the A-B transition in water, ethanolic mixtures, and with hexaaminecobalt(III), and characterized RNA and RNA-DNA duplex structure. The results were encouraging, however we had not fully converged the simulations. As we got to bigger and faster computers (Cray T3D, Cray T3E, IBM SP-2, …) longer and longer simulations started to expose deficiencies in the AMBER nucleic acid force fields. From ~1998-recent time, the community has worked hard to overcome those deficiencies. Recent work highlights testing of Mg2+, development of force field parameters for natual and unnaturally modified nucleotides, and further force field testing on a variety of systems.