OpenFF 2.2.1 Relative Binding Free Energy Benchmarks

Overview

Relative binding free energy benchmarks of the openff-2.2.1 release using the JACS set from (https://github.com/OpenFreeEnergy/IndustryBenchmarks2024).

Contents

Benchmark variants

The following benchmark variants were run:
  * `openff-2.2.1_elf10`: simulations using OpenFF 2.2.1 and AM1BCCELF10 charges using the OpenEye Toolkit.
  * `openff-2.2.1_nagl`: simulations using OpenFF 2.2.1 and AshGC v0.1rc3 charges
  * `openff-2.2.1_am1bcc`: simulations using OpenFF 2.2.1 and AM1BCC charges calculated using ambertools. Please note that these charges were not assigned to the input conformer, but rather a conformer that was generated at charge assignment time via RDKit through the OpenFF toolkit.

RBFE data

The `data` folder contains all the ddG data for each transformation in each set. These are stored as TSV files within subdirectories for each system in the JACS set.

Per system data files

These are stored as TSV files within subdirectories for each system in the JACS set.
Reference CSV data (labelled as `{system}_ref.csv`), taken from the Ross et al. 2023 dataset (https://github.com/schrodinger/public_binding_free_energy_benchmark)
can alsos be found.

Aggregate dG and ddG files

CSV files with all the dG and ddG values for all datasets can be found in `data`.

Simulation details

* All simulations were carried out using the RelativeHybridTopology protocol in OpenFE v1.4.
* Mappings were created using Kartograf, these are the same as those used in the OpenFE industry benchmarks.
* Transformation edges were created using Lomap, these are the same as those used in the OpenFE industry benchmarks.
* Simulations used openfe default settings, except the following:
  * Dodecahedron solvent box with 1 nm padding in complex and 1.5 nm padding in solvent
  * 2.5 ps HREX exchange rate
  * 0.9 nm short range interaction cutoff