Your browser doesn't support javascript.
loading
Development and Testing of the OPLS-AA/M Force Field for RNA.
Robertson, Michael J; Qian, Yue; Robinson, Matthew C; Tirado-Rives, Julian; Jorgensen, William L.
Afiliação
  • Robertson MJ; Department of Chemistry , Yale University , New Haven , Connecticut 06520-8107 , United States.
  • Qian Y; Department of Chemistry , Yale University , New Haven , Connecticut 06520-8107 , United States.
  • Robinson MC; Department of Chemistry , Yale University , New Haven , Connecticut 06520-8107 , United States.
  • Tirado-Rives J; Department of Chemistry , Yale University , New Haven , Connecticut 06520-8107 , United States.
  • Jorgensen WL; Department of Chemistry , Yale University , New Haven , Connecticut 06520-8107 , United States.
J Chem Theory Comput ; 15(4): 2734-2742, 2019 Apr 09.
Article em En | MEDLINE | ID: mdl-30807148
ABSTRACT
Significant improvements have been made to the OPLS-AA force field for modeling RNA. New torsional potentials were optimized based on density functional theory (DFT) scans at the ωB97X-D/6-311++G(d,p) level for potential energy surfaces of the backbone α and γ dihedral angles. In combination with previously reported improvements for the sugar puckering and glycosidic torsion terms, the new force field was validated through diverse molecular dynamics simulations for RNAs in aqueous solution. Results for dinucleotides and tetranucleotides revealed both accurate reproduction of 3 J couplings from NMR and the avoidance of several unphysical states observed with other force fields. Simulations of larger systems with noncanonical motifs showed significant structural improvements over the previous OPLS-AA parameters. The new force field, OPLS-AA/M, is expected to perform competitively with other recent RNA force fields and to be compatible with OPLS-AA models for proteins and small molecules.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Oligonucleotídeos / RNA Idioma: En Ano de publicação: 2019 Tipo de documento: Article

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Oligonucleotídeos / RNA Idioma: En Ano de publicação: 2019 Tipo de documento: Article