title: A new AMBER-compatible force field parameter set for alkanes.
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.
authors.affiliation: Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Moscow, 119991, Russia, agilemolecule@gmail.com.
authors.forename: Alexei M
authors.initials: AM
authors.lastname: Nikitin
authors.forename: Yury V
authors.initials: YV
authors.lastname: Milchevskiy
authors.forename: Alexander P
authors.initials: AP
authors.lastname: Lyubartsev
mesh_terms: D000473:Alkanes / Q000737:chemistry*; D000596:Amino Acids / Q000737:chemistry; D003198:Computer Simulation; D008055:Lipids / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D015394:Molecular Structure; D012984:Software; D012995:Solubility; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D000473:Alkanes; D000596:Amino Acids; D008055:Lipids; D012997:Solvents