2026-02-12-Sage-230-JACS

OpenFE RBFE - jacs_set (8 systems) - 2026-02-12_sage_230_jacs_set Description Re-run of the JACS-set using the openfe relative hybrid topology protocol with Sage-2.3.0 and AshGC partial charges. Overview RBFE benchmark results prepared from AlchemicalArchive JSON file(s) generated with OpenFE and Alchemiscale. This submission describes the jacs_set RBFE benchmark prepared with ff14SB/phosaa10/tip3p_HFE_multivalent/tip3p_standard for proteins and solvents, and openff-2.3.0 with nagl_openff-gnn-am1bcc-1.0.0.pt for ligands, solutes, and cofactors. The network the entire JACS set. Results are derived from archived Alchemiscale workflow data. Software Versions openfe_version: 1.8.0 openmm_version: 8.2.0 openff_toolkit_version: 0.18.0 Alchemical Network Keys: - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191: jacs_set/p38 - AlchemicalNetwork-139c105576710380f915128235c1f5fe: jacs_set/cdk2 - AlchemicalNetwork-459636b551faa8c08cb10104bc4dfdc4: jacs_set/jnk1 - AlchemicalNetwork-46de554347d878943aab14579ab1d29a: jacs_set/mcl1 - AlchemicalNetwork-dc1002e80f494ee62dd88b3a1c16775b: jacs_set/bace - AlchemicalNetwork-ed08b22af2e51875d23b0283d2080252: jacs_set/tyk2 - AlchemicalNetwork-f22ccb1e62958618618125f80e8d43e7: jacs_set/ptp1b - AlchemicalNetwork-ff86d1ac92ee7d1e5ae8bc469370530b: jacs_set/thrombin Recommended Descriptors forcefield: ["ff14SB", "phosaa10", "tip3p_HFE_multivalent", "tip3p_standard"] small_molecule_forcefield: "openff-2.3.0" partial_charges: ""nagl_openff-gnn-am1bcc-1.0.0.pt" mapper: "KartografAtomMapper 1.2.0 (LSA)" BenchmarkData provenance (from openfe-benchmarks planning script) with associated network key benchmark_data: source_repository: https://github.com/OpenFreeEnergy/openfe-benchmarks "jacs_set": "bace": AlchemicalNetwork-dc1002e80f494ee62dd88b3a1c16775b "cdk2": AlchemicalNetwork-139c105576710380f915128235c1f5fe "jnk1": AlchemicalNetwork-459636b551faa8c08cb10104bc4dfdc4 "mcl1": AlchemicalNetwork-46de554347d878943aab14579ab1d29a "p38": AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 "ptp1b": AlchemicalNetwork-f22ccb1e62958618618125f80e8d43e7 "thrombin": AlchemicalNetwork-ff86d1ac92ee7d1e5ae8bc469370530b "tyk2": AlchemicalNetwork-ed08b22af2e51875d23b0283d2080252 Protocol Settings protocol_settings: - protocol: "RelativeHybridTopologyProtocol" timestep: "4.0 fs" temperature: "298.15 K" pressure: "1 bar" forcefields: ["ff14SB", "phosaa10", "tip3p_HFE_multivalent", "tip3p_standard"] small_molecule_forcefield: "openff-2.3.0" partial_charges: "nagl_openff-gnn-am1bcc-1.0.0.pt" equilibration_time: "1.0 ns" production_time: "5.0 ns" vacuum_equilibration_time: vacuum_production_time: solvent_equilibration_time: solvent_production_time: lambda_functions: "default" lambda_windows: "11" lambda_schedule: "" notes: | Applies to 283 edges: - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 jacs_set-p38: ligand_start=2aa, ligand_final=3flq, solvent={'O'}, cofactors=none, protein=none - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 jacs_set-p38: ligand_start=2aa, ligand_final=3flw, solvent={'O'}, cofactors=none, protein=none - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 jacs_set-p38: ligand_start=2aa, ligand_final=3fly, solvent={'O'}, cofactors=none, protein=none - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 jacs_set-p38: ligand_start=2bb, ligand_final=2v, solvent={'O'}, cofactors=none, protein=none - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 jacs_set-p38: ligand_start=2c, ligand_final=3flz, solvent={'O'}, cofactors=none, protein=none - etc. - protocol: "RelativeHybridTopologyProtocol" notes: | Detailed protocol settings differ: - solvation_settings.solvent_padding: 1.5 -> 1 Applies to 283 edges: - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 jacs_set-p38: ligand_start=2aa, ligand_final=3flq, solvent={'O'}, cofactors=none, protein={'unknown'} - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 jacs_set-p38: ligand_start=2aa, ligand_final=3flw, solvent={'O'}, cofactors=none, protein={'unknown'} - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 jacs_set-p38: ligand_start=2aa, ligand_final=3fly, solvent={'O'}, cofactors=none, protein={'unknown'} - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 jacs_set-p38: ligand_start=2bb, ligand_final=2v, solvent={'O'}, cofactors=none, protein={'unknown'} - AlchemicalNetwork-034843fe04133cac65ec83f9b73fc191 jacs_set-p38: ligand_start=2c, ligand_final=3flz, solvent={'O'}, cofactors=none, protein={'unknown'} - etc. Rights - License: CC-BY-4.0