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A new AMBER-compatible force field parameter set for alkanes

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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.

We have a new force field parameter set applicable to various alkanes, including short and long chains, branches, as well as flexible or rigidly strained rings. The new set proves consistent, in agreement with ab-initio computations and experiment, description of conformational behavior, and thermodynamic physical properties.

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Acknowledgments

This work has been carried out with the financial support of the Program of the Presidium of the Russian Academy of Sciences for Molecular and Cellular Biology and the Russian Foundation for Basic Research (Grant No. 11-04-02001), and Swedish Research Council (Vetenskapsrådet, Grant 621-2010-5005). The authors are grateful to Alexander V. Galkin for helpful comments and rendering the paper into English.

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Authors and Affiliations

  1. Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Moscow, 119991, Russia

    Alexei M. Nikitin & Yury V. Milchevskiy

  2. Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, 10691, Sweden

    Alexander P. Lyubartsev

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  1. Alexei M. Nikitin
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  2. Yury V. Milchevskiy
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  3. Alexander P. Lyubartsev
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Correspondence to Alexei M. Nikitin.

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Nikitin, A.M., Milchevskiy, Y.V. & Lyubartsev, A.P. A new AMBER-compatible force field parameter set for alkanes. J Mol Model 20, 2143 (2014). https://doi.org/10.1007/s00894-014-2143-6

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