Development of polyphosphate parameters for use with the AMBER force field

J Comput Chem. 2003 Jul 15;24(9):1016-25. doi: 10.1002/jcc.10262.

Abstract

Accurate force fields are essential for reproducing the conformational and dynamic behavior of condensed-phase systems. The popular AMBER force field has parameters for monophosphates, but they do not extend well to polyphorylated molecules such as ADP and ATP. This work presents parameters for the partial charges, atom types, bond angles, and torsions in simple polyphosphorylated compounds. The parameters are based on molecular orbital calculations of methyldiphosphate and methyltriphosphate at the RHF/6-31+G* level. The new parameters were fit to the entire potential energy surface (not just minima) with an RMSD of 0.62 kcal/mol. This is exceptional agreement and a significant improvement over the current parameters that produce a potential surface with an RMSD of 7.8 kcal/mol to that of the ab initio calculations. Testing has shown that the parameters are transferable and capable of reproducing the gas-phase conformations of inorganic diphosphate and triphosphate. Also, the parameters are an improvement over existing parameters in the condensed phase as shown by minimizations of ATP bound in several proteins. These parameters are intended for use with the existing AMBER 94/99 force field, and they will permit users to apply AMBER to a wider variety of important enzymatic systems.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adenosine Triphosphate / chemistry
  • Algorithms
  • Computer Simulation
  • Models, Molecular*
  • Molecular Conformation*
  • Nucleotides / chemistry*
  • Organophosphorus Compounds / chemistry*
  • Phosphates / chemistry*
  • Protein Binding
  • Proteins / chemistry*
  • Thermodynamics

Substances

  • Nucleotides
  • Organophosphorus Compounds
  • Phosphates
  • Proteins
  • Adenosine Triphosphate