Nucleic Acid Force Fields

For a full description of the force fields and how to load them, please read Chapter 3 of the Amber Reference Manual.

DNA - OL15

The OL15 parameters are recommended for simulating DNA. A full explanation can be found here including a comparison of results with TIP3P and OPC water models.

Ref: R. Galindo-Murillo; J. C. Robertson; M. Zgarbovic; J. Sponer; M. Otyepka; P. Jureska; T. E. Cheatham. Assessing the Current State of Amber Force Field Modifications for DNA. J. Chem. Theory Comput., 2016, 12, 4114–4127.

RNA - OL3

The OL3 parameters are recommended for simulating RNA.

Ref: M. Zgarbova; M. Otyepka; J. Sponer; A. Mladek; P. Banas; T. E. Cheatham; P. Jurecka. Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. J. Chem. Theory Comput., 2011, 7, 2886–2902.

RNA - OL3 with Steinbrecher and Case Phosphate Oxygens

It has been shown that the OL3 parameter set in combination with the Steinbrecher and Case phosphate oxygen van der Waals radii work best in combination with the OPC water model to model RNA. The leaprc.RNA.LJbb file will load this combination.

Ref: C. Bergonzo; T. E. Cheatham III. Improved force field parameters lead to a better description of RNA structure. J. of Chem. Theory Comput., 2015, 11, 3969–3972.

Modified RNA Force Fields

This paper describes the modified RNA base parameters from John SantaLucia and Berny Schlegel at Wayne State. These are compatible with the ff94.dat and ff99.dat RNA parameters and do not contain the more recent (post 2006) force field improvements to torsions and atomic radii.