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Journal of Computer-Aided Molecular Design

, Volume 9, Issue 3, pp 251–268 | Cite as

MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry

  • Paul R. Gerber
  • Klaus Müller
Research Papers

Summary

The mathematical formulation, parametrization scheme, and structural results of a new, generally applicable molecular force field are presented. The central features are a scheme for automatic parameter assignments, the consistent united-atom approximation, the absence of atom types other than elements, the replacement of electrostatic terms by geometrical hydrogen-bonding terms, the concomitant lack of a need for partial atomic charge assignment and the strict adherence to a finite-range design. As a consequence of omitting all hydrogen atoms, optimal hydrogen-bond patterns are computed dynamically by appropriate network analyses. For a test set of 1589 structures, selected from the Cambridge Structural Database solely on the grounds of a given element list and criteria for high structure refinement, the agreements are on average 2 pm for bonds, 2° for valence angles and 10 to 20 pm for the root-mean-square deviation of atom positions, depending somewhat on size and flexibility of the structures. More qualitative testing of large-scale structural properties of the force field on proteins and DNA oligomers revealed satisfactory performance.

Keywords

Force field Potential energy function Molecular structure Molecular modelling 

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Copyright information

© ESCOM Science Publishers B.V 1995

Authors and Affiliations

  • Paul R. Gerber
    • 1
  • Klaus Müller
    • 1
  1. 1.Pharmaceutical Research and DevelopmentF. Hoffmann-La Roche AGBaselSwitzerland

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