Automation of AMOEBA polarizable force field parameterization for small molecules

Johnny C. Wu, Gaurav Chattree, Pengyu Ren

Research output: Contribution to journalArticlepeer-review

130 Citations (Scopus)


A protocol to generate parameters for the AMOEBA polarizable force field for small organic molecules has been established, and polarizable atomic typing utility, Poltype, which fully automates this process, has been implemented. For validation, we have compared with quantum mechanical calculations of molecular dipole moments, optimized geometry, electrostatic potential, and conformational energy for a variety of neutral and charged organic molecules, as well as dimer interaction energies of a set of amino acid side chain model compounds. Furthermore, parameters obtained in gas phase are substantiated in liquid-phase simulations. The hydration free energy (HFE) of neutral and charged molecules have been calculated and compared with experimental values. The RMS error for the HFE of neutral molecules is less than 1 kcal/mol. Meanwhile, the relative error in the predicted HFE of salts (cations and anions) is less than 3% with a correlation coefficient of 0.95. Overall, the performance of Poltype is satisfactory and provides a convenient utility for applications such as drug discovery. Further improvement can be achieved by the systematic study of various organic compounds, particularly ionic molecules, and refinement and expansion of the parameter database.

Original languageEnglish
Article number1138
Pages (from-to)1-11
Number of pages11
JournalTheoretical Chemistry Accounts
Issue number3
Publication statusPublished - Mar 1 2012
Externally publishedYes


  • Atomic typer
  • Molecular dynamics
  • Polarizable force field
  • Poltype
  • Small molecule modeling

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry


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