Symmetrization of the AMBER and CHARMM force fields

@article{Malolepsza2010SymmetrizationOT,
  title={Symmetrization of the AMBER and CHARMM force fields},
  author={E. Malolepsza and B. Strodel and M. Khalili and S. Trygubenko and S. Fejer and D. Wales},
  journal={Journal of Computational Chemistry},
  year={2010},
  volume={31}
}
The AMBER and CHARMM force fields are analyzed from the viewpoint of the permutational symmetry of the potential for feasible exchanges of identical atoms and chemical groups in amino and nucleic acids. In each case, we propose schemes for symmetrizing the potentials, which greatly facilitate the bookkeeping associated with constructing kinetic transition networks via geometry optimization. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 
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  • F. Rao
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  • J. Comput. Chem.
  • 2011
  • 4
  • PDF
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  • 21
  • PDF
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  • 16
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  • D. Wales, J. Carr
  • Medicine, Chemistry
  • Journal of chemical theory and computation
  • 2012
  • 19
  • PDF
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  • 1
  • PDF
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  • 24
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...
1
2
3
...

References

SHOWING 1-10 OF 39 REFERENCES
The Amber biomolecular simulation programs
  • 5,648
  • PDF
All-atom empirical potential for molecular modeling and dynamics studies of proteins.
  • 10,450
  • PDF
...
1
2
3
4
...