Atomic properties of amino acids: Computed atom types as a guide for future force-field design

Paul L A Popelier, Fiona M. Aicken

    Research output: Contribution to journalArticlepeer-review


    The quantum chemical topology (QCT) is able to propose atom types by direct computation rather than by chemical intuition. In previous work, molecular electron densities of 20 amino acids and smaller derived molecules were partitioned into a set of 760 topological atoms. Each atoms was characterised by seven atomic properties and subjected to cluster analysis element by element, that is, C, H, O, N, and S. From the respective dendrograms, 21 carbon atom types were distinguished, 7 hydrogen, 2 nitrogen, 6 oxygen, and 6 sulfur atom types. Herein, we contrast the QCT atoms types with those of the assisted model building with energy refinement (AMBER) force field. We conclude that in spite of fair agreement between QCT and AMBER atom types, the latter are sometimes underdifferentiated and sometimes overdifferentiated. In summary, we suggest that QCT is a useful guide in designing new force fields or improving existing ones. The computational origin of QCT atom types makes their determination unbiased compared to atom type determination by chemical intuition and a priori assumption. We provide a list of specific recommendations.
    Original languageEnglish
    Pages (from-to)824-829
    Number of pages5
    Issue number8
    Publication statusPublished - 18 Aug 2003


    • Amino acids
    • Cluster analysis
    • Density functional calculations
    • Force fields
    • Quantum chemistry
    • Topology


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