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Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software

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Khalak,  Y
Research Group of Computational Biomolecular Dynamics, MPI for Biophysical Chemistry, Max Planck Society;

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de Groot,  B. L.
Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society;

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Gapsys,  V.
Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society;

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Citation

Khalak, Y., Tresadern, G., de Groot, B. L., & Gapsys, V. (2021). Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software. Journal of Computer-Aided Molecular Design, 35(1), 49-61. doi:10.1007/s10822-020-00359-1.


Cite as: https://hdl.handle.net/21.11116/0000-0009-5A32-A
Abstract
In the current work we report on our participation in the SAMPL7 challenge calculating absolute free energies of the host–guest systems, where 2 guest molecules were probed against 9 hosts-cyclodextrin and its derivatives. Our submission was based on the non-equilibrium free energy calculation protocol utilizing an averaged consensus result from two force fields (GAFF and CGenFF). The submitted prediction achieved accuracy of 1.38kcal/mol in terms of the unsigned error averaged over the whole dataset. Subsequently, we further report on the underlying reasons for discrepancies between our calculations and another submission to the SAMPL7 challenge which employed a similar methodology, but disparate ligand and water force fields. As a result we have uncovered a number of issues in the dihedral parameter definition of the GAFF 2 force field. In addition, we identified particular cases in the molecular topologies where different software packages had a different interpretation of the same force field. This latter observation might be of particular relevance for systematic comparisons of molecular simulation software packages. The aforementioned factors have an influence on the final free energy estimates and need to be considered when performing alchemical calculations.