Structures and data for https://doi.org/10.1039/D1SC03472C
Throughout this work a modified version of gromacs 2019.4 was used, fixing a bug (gmx issue 3403) with how the free energy kernel handled exclusions beyond the electrostatic cutoff. The code is available in the fix_for_gmx_2019.4 folder.
Most of the absolute free energy calculations were carried out with an automated workflow available separately here: https://github.com/deGrootLab/pmx/tree/abs_dG_workflow/src/pmx/scripts/workflows A manual and a working example of the workflows use is available in the workflow_example folder.
These are found in the other folders herein, named by the corresponding protein. These folders also include text files with the final results for the calcualtions.