Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics.

ABSTRACT: The backbone dihedral parameters of the Amber RNA force field were improved by fitting using multiple linear regression to potential energies determined by quantum chemistry calculations. Five backbone and four glycosidic dihedral parameters were fit simultaneously to reproduce the potential energies determined by a high-level density functional theory calculation (B97D3 functional with the AUG-CC-PVTZ basis set). Umbrella sampling was used to determine conformational free energies along the dihedral angles, and these better agree with the population of conformations observed in the protein data bank for the new parameters than for the conventional parameters. Molecular dynamics simulations performed on a set of hairpin loops, duplexes and tetramers with the new parameter set show improved

SUBMITTER: Aytenfisu AH 

PROVIDER: S-EPMC5312698 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature