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

• Published in: Life (Basel, Switzerland) Switzerland), 2022-04, Vol.12 (5), p.666
• Main Authors: Schneider, Amelia L, Albrecht, Amanda V, Huang, Kenneth, Germann, Markus W, Poon, Gregory M K
• Format: Article
• Language: English
• Subjects: ab initio methods; Acids; charge; Deoxyribonucleic acid; Derivation; DNA; electrostatic potential; Molecular dynamics; NMR spectroscopy; Nucleic acids; Optimization; Parameterization; Polymers; Quantum mechanics; Residues; Structural models
• ISSN: 2075-1729; 2075-1729
• DOI: 10.3390/life12050666

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 structures for charge derivation. Instead, structures from molecular mechanics minimization yield charges with up to 6-fold lower RMS deviation from the published values, due to the choice of such an approach in the derivation of the original charge set. We present a contemporary protocol for rendering self-consistent charges as well as optimized charges for a panel of nine non-canonical residues that will permit comparison with literature as well as studying the dynamics of novel DNA polymers.