Assessing the Current State of Amber Force Field Modifications for DNAR2023 Edition

Advances in moleculardynamics (MD) software alongside enhancedcomputational power and hardware have allowed for MD simulations tosignificantly expand our knowledge of biomolecular structure, dynamics,and interactions. Furthermore, it has allowed for the extension ofconformational sampling times from nanoseconds to the microsecondlevel and beyond. This has not only made convergence of conformationalensembles through comprehensive sampling possible but consequentlyexposed deficiencies and allowed the community to overcome limitationsin the available force fields. The reproducibility and accuracy ofthe force fields are imperative in order to produce biologically relevantdata. The Amber nucleic acid force fields have been used widely sincethe mid-1980s, and improvement of these force fields has been a communityeffort with several artifacts revealed, corrected, and reevaluatedby various research groups. Here, we focus on the Amber force fieldsfor use with double-stranded DNA and present the assessment of tworecently developed force field parameter sets (OL21 and Tumuc1). ExtensiveMD simulations were performed with six test systems and two differentwater models. We observe the improvement of OL21 and Tumuc1 comparedto previous generations of the Amber DNA force. We did not detectany significant improvement in the performance of Tumuc1 comparedto OL21 despite the reparameterization of bonded force field termsin the former; however, we did note discrepancies in Tumuc1 when modelingZ-DNA sequences.