English
 
Help Privacy Policy Disclaimer
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT

Released

Journal Article

Evaluating nonpolarizable nucleic acid force fields: A systematic comparison of the nucleobases hydration free energies and water-chloroform partition coefficients.

MPS-Authors
/persons/resource/persons41407

Wolf,  M. G.
Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society;

/persons/resource/persons15149

Groenhof,  G.
Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society;

External Resource
Fulltext (restricted access)
There are currently no full texts shared for your IP range.
Fulltext (public)

1563138.pdf
(Publisher version), 356KB

Supplementary Material (public)

1563138-Suppl.pdf
(Supplementary material), 206KB

Citation

Wolf, M. G., & Groenhof, G. (2012). Evaluating nonpolarizable nucleic acid force fields: A systematic comparison of the nucleobases hydration free energies and water-chloroform partition coefficients. Journal of Computational Chemistry, 33(28), 2225-2232. doi:10.1002/jcc.23055.


Cite as: https://hdl.handle.net/11858/00-001M-0000-0010-15E9-3
Abstract
Nucleic acid force fields have been shown to reproduce structural properties of DNA and RNA very well, but comparative studies with respect to thermodynamic properties are rare. As a test for thermodynamic properties, we have computed hydration free energies and chloroform-to-water partition coefficients of nucleobases using the AMBER-99, AMBER-gaff, CHARMM-27, GROMOS-45a4/53a6 and OPLS-AA force fields. A mutual force field comparison showed a very large spread in the calculated thermodynamic properties, demonstrating that some of the parameter sets require further optimization. The choice of solvent model used in the simulation does not have a significant effect on the results. Comparing the hydration free energies obtained by the various force fields to the adenine and thymine experimental values showed a very large deviation for the GROMOS and AMBER parameter sets. Validation against experimental partition coefficients showed good agreement for the CHARMM-27 parameter set. In view of mutation studies, differences in partition coefficient between two bases were also compared, and good agreement between experiments and calculations was found for the AMBER-99 parameter set. Overall, the CHARMM-27 parameter set performs best with respect to the thermodynamic properties tested here. © 2012 Wiley Periodicals, Inc.