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

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 [Formula: see text] 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

SUBMITTER: Khalak Y 

PROVIDER: S-EPMC7862541 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature