Journal of Biomolecular NMR

, Volume 3, Issue 1, pp 55–66 | Cite as

Structure refinement using time-averaged J-coupling constant restraints

  • Andrew E. Torda
  • Roger M. Brunne
  • Thomas Huber
  • Horst Kessler
  • Wilfred F. van Gunsteren
Research Papers


We describe a new penalty function for use in restrained molecular dynamics simulations which allows experimental J-coupling information to be enforced as a time-averaged, rather than instantaneous, quantity. The pseudo-energy term has been formulated in terms of a calculated J value (a measured quantity) rather than the relevant dihedral angle (a derived quantity). This accounts for the distinct non-linearity of the coupling constant with respect to either Cartesian coordinates or dihedral angles. Example simulations of the cyclic decapeptide antamanide show the procedure's ability to enforce experimental restraints while exploring a large region of conformational space and producing a relatively small disturbance of the physical force field.


J-coupling Time averaging Structure refinement Computer simulation Molecular dynamics 



molecular dynamics




nuclear Overhauser effect


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Copyright information

© ESCOM Science Publishers B.V 1993

Authors and Affiliations

  • Andrew E. Torda
    • 1
  • Roger M. Brunne
    • 1
  • Thomas Huber
    • 2
  • Horst Kessler
    • 2
  • Wilfred F. van Gunsteren
    • 1
  1. 1.Physical Chemistry (Computational Chemistry)ETH ZentrumZürichSwitzerland
  2. 2.Organisch-Chemisches InstitutTechnische Universität MünchenGarchingGermany

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