Parameters of monovalent ions in the AMBER-99 forcefield: assessment of inaccuracies and proposed improvements.
The monovalent ion parameters used by the AMBER-99 forcefield are shown to exhibit physically inaccurate behavior in molecular dynamics simulations of strong 1:1 electrolytes. These errors arise from an ad hoc adaptation of Aqvist's cation parameters. The result is the rapid formation of large, unphysical clusters at concentrations that are well below solubility limits. The observed unphysical behavior poses a serious challenge for simulating ions around highly charged polymers such as nucleic acids. In this communication, we explain the source of this unphysical behavior. To facilitate the continued use of the popular AMBER parameters, we prescribe a simple fix whereby Aqvist's cations and anions are used in conjunction with the AMBER forcefield for nucleic acids. A preliminary test of this strategy suggests that the proposed fix is reasonable and is likely to be generalizable for simulating diffuse and specific ion binding to nucleic acids.
Chen
Alan A
AA
Molecular Biophysics Program & Center for Computational Biology, Washington University School of Medicine, St Louis, MO 63110, USA.
Pappu
Rohit V
RV
D002412:Cations / Q000737:chemistry; D007477:Ions / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D009930:Organic Chemicals / Q000737:chemistry*; D011188:Potassium / Q000737:chemistry; D012964:Sodium / Q000737:chemistry; D012996:Solutions
D002412:Cations; D007477:Ions; D009930:Organic Chemicals; D012996:Solutions; D012964:Sodium; D011188:Potassium