Petr Jurečka

Palacký University Olomouc, Department of Physical Chemistry, Research

New AMBER Force Fields for More Reliable DNA and Protein–DNA Simulations

Abstract The latest addition of the OL family of force fields, OL24, improves the description of the A/B-DNA equilibrium. Existing AMBER force field variants underpopulate the north (C3′-endo) sugar pucker, compromising simulations of protein–DNA systems requiring B-to-A transitions. The OL24 refinement of deoxyribose puckering brings the A/B equilibrium into better agreement with experimental data. The description of canonical B-DNA, DNA–RNA hybrids, and protein-induced conformational adaptation is also improved. Combined with the previous α/γ correction of OL21, OL24 provides a coherent framework for general DNA and protein–DNA simulations. We also assess the compatibility of OL force fields with Electronic Continuum Correction (ECC) charge scaling and the usefulness of Lorentz-Berthelot combining rules.