A new AMBER-compatible force field parameter set for alkanes

J Mol Model. 2014 Mar;20(3):2143. doi: 10.1007/s00894-014-2143-6. Epub 2014 Feb 19.

Abstract

We present a new force field parameter set for simulating alkanes. Its functional form and parameters are chosen to make it directly compatible with the AMBER94/99/12 family of force fields implemented in the available software. The proposed parameterization enables universal description of both the conformational and thermodynamic properties of linear, branched, and cyclic alkanes. Such unification is achieved by using two essential principles: (1) reduction of the Lennard-Jones radius for all sp3 carbons to 1.75Å; (2) separate optimization of Lennard-Jones well depths for carbons with different degree of substitution. The new parameter set may prove to be optimal for description of alkyl residues in a broad range of biomolecules, from amino acids to lipids with their extended linear tails.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alkanes / chemistry*
  • Amino Acids / chemistry
  • Computer Simulation*
  • Lipids / chemistry
  • Models, Molecular*
  • Molecular Conformation
  • Molecular Structure
  • Software*
  • Solubility
  • Solvents / chemistry
  • Thermodynamics

Substances

  • Alkanes
  • Amino Acids
  • Lipids
  • Solvents