├── .gitignore ├── LICENSE ├── README.md ├── abfe ├── __init__.py ├── abfe_alchemy_analysis.py ├── abfe_alchemy_md.py ├── abfe_alchemy_morph.py ├── abfe_equilibration.py ├── abfe_main.py ├── abfe_topology.py ├── biochemsystems.py ├── const.py ├── md │ ├── __init__.py │ ├── amber_alchemy_mdin.py │ ├── amber_mdin.py │ ├── analytic.py │ ├── charge_correction.py │ ├── cpptraj_tools.py │ └── md_tools.py └── utils │ ├── __init__.py │ ├── alchemlyb_dUoverlap.py │ ├── check_md_jobs.py │ └── common_tools.py ├── environment_abfe.yml └── testing ├── abfe_testing ├── config.yaml ├── ligands.in ├── ligands │ ├── bnz │ │ └── ligand.sdf │ └── phn │ │ └── ligand.sdf ├── proteins │ └── 181L │ │ └── protein.pdb └── submitBFE.sh └── ahfe_testing ├── config.yaml ├── ligands.in ├── ligands ├── bnz │ └── ligand.sdf └── phn │ └── ligand.sdf └── submitBFE.sh /.gitignore: -------------------------------------------------------------------------------- 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