Self-Consistent Parameterization of DNA Residues for the Non-Polarizable AMBER Force Fields.

ABSTRACT: Fixed-charge (non-polarizable) forcefields are accurate and computationally efficient tools for modeling the molecular dynamics of nucleic acid polymers, particularly DNA, well into the µs timescale. The continued utility of these forcefields depends in part on expanding the residue set in step with advancing nucleic acid chemistry and biology. A key step in parameterizing new residues is charge derivation which is self-consistent with the existing residues. As atomic charges are derived by fitting against molecular electrostatic potentials, appropriate structural models are critical. Benchmarking against the existing charge set used in current AMBER nucleic acid forcefields, we report that quantum mechanical models of deoxynucleosides, even at a high level of theory, are not optimal struc

SUBMITTER: Schneider AL 

PROVIDER: S-EPMC9143812 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature