Journal of Computer-Aided Molecular Design

, Volume 26, Issue 5, pp 517–525 | Cite as

Prediction of SAMPL3 host–guest binding affinities: evaluating the accuracy of generalized force-fields

  • Hari S. Muddana
  • Michael K. Gilson


We used the second-generation mining minima method (M2) to compute the binding affinities of the novel host–guest complexes in the SAMPL3 blind prediction challenge. The predictions were in poor agreement with experiment, and we conjectured that much of the error might derive from the force field, CHARMm with Vcharge charges. Repeating the calculations with other generalized force-fields led to no significant improvement, and we observed that the predicted affinities were highly sensitive to the choice of force-field. We therefore embarked on a systematic evaluation of a set of generalized force fields, based upon comparisons with PM6-DH2, a fast yet accurate semi-empirical quantum mechanics method. In particular, we compared gas-phase interaction energies and entropies for the host–guest complexes themselves, as well as for smaller chemical fragments derived from the same molecules. The mean deviations of the force field interaction energies from the quantum results were greater than 3 kcal/mol and 9 kcal/mol, for the fragments and host–guest systems respectively. We further evaluated the accuracy of force-fields for computing the vibrational entropies and found the mean errors to be greater than 4 kcal/mol. Given these errors in energy and entropy, it is not surprising in retrospect that the predicted binding affinities deviated from the experiment by several kcal/mol. These results emphasize the need for improvements in generalized force-fields and also highlight the importance of systematic evaluation of force-field parameters prior to evaluating different free-energy methods.


SAMPL3 Binding affinity Supramolecular Host–guest Force-field Mining minima Semi-empirical 



This publication was made possible by grant no.GM061300 from NIH. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH.


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© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  1. 1.Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San DiegoLa JollaUSA

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