Skip to main content
Log in

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

  • Research Papers
  • Published:
Journal of Computer-Aided Molecular Design Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Li, J.H. and Allinger, N.L., J. Comput. Chem., 12 (1991) 186.

    Google Scholar 

  2. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S. and Karplus, M., J. Comput. Chem., 4 (1983) 187.

    Google Scholar 

  3. Momany, F.A., McGuire, R.F., Burgess, A.W. and Scheraga, H.A., J. Phys. Chem., 79 (1975) 2361.

    Google Scholar 

  4. Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., ProfetaJr., S. and Weiner, P., J. Am. Chem. Soc., 106 (1984) 765.

    Google Scholar 

  5. Van, Gunsteren, W.F. and Berendsen, H.J.C., GROMOS, Biomos, Groningen, 1987.

    Google Scholar 

  6. Maple, J.R., Dinur, U. and Hagler, A.T., Proc. Natl. Acad. Sci. USA, 85 (1988) 5350.

    Google Scholar 

  7. Clark, M., CramerIII, R.D. and Van, Opdenbosch, N., J. Comput. Chem., 10 (1989) 982.

    Google Scholar 

  8. Momany, F.A. and Rone, R., J. Comput. Chem., 13 (1992) 888.

    Google Scholar 

  9. Taylor, R. and Kennard, O., J. Am. Chem. Soc., 105 (1983) 5761.

    Google Scholar 

  10. Vedani, A. and Dunitz, J.D., J. Am. Chem. Soc., 107 (1985) 7653.

    Google Scholar 

  11. Heilbronner, E. and Bock, H., The HMO Model and its Application, Wiley, London, 1976.

    Google Scholar 

  12. Trinajstic, N., Chemical Graph Theory, CRC Press, Boca Raton, FL, 1983.

    Google Scholar 

  13. Callomon, J.H., Hirota, E., Kuchitsu, K., Lafferty, W.J., Maki, A.G. and Pote, C.S., In Hellwege, K.H. (Ed.) Landolt-Börstein, Vol. 7: Structure Data of Free Polyatomic Molecules, Springer, Berlin, 1976.

    Google Scholar 

  14. Allen, F.H., Bellard, S., Brice, M.D., Cartwright, B.A., Doubleday, A., Higgs, H., Hummelink, T., Hummelink-Peters, B.G., Kennard, O., Motherwell, W.D.S., Rogers, J.R. and Watson, D.G., Acta Crystallogr., B35 (1979) 2331.

    Google Scholar 

  15. Allred, A.L. and Rochow, E.G., J. Inorg. Nucl. Chem., 5 (1958) 264.

    Google Scholar 

  16. Powell, M.J.D., Math. Programming, 12 (1977) 241.

    Google Scholar 

  17. Ramanadham, M., Sieker, L.C. and Jensen, L.H., Acta Crystallogr., A37 (1981) 33.

    Google Scholar 

  18. Fratini, A.V., Kopka, M.L., Drew, H.R. and Dickerson, R.E., J. Biol. Chem., 257 (1982) 14686.

    Google Scholar 

  19. Matthews, D.A., Bolin, J.T., Burridge, J.M., Filman, D.J., Volz, K.W., Kaufman, B.T., Bedell, C.R., Champness, J.N., Stammers, D.K. and Kraut, J., J. Biol. Chem., 260 (1985) 381.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Gerber, P.R., Müller, K. MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry. J Computer-Aided Mol Des 9, 251–268 (1995). https://doi.org/10.1007/BF00124456

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00124456

Keywords

Navigation