├── .gitignore ├── LICENSE ├── MDP_files ├── absolute_solvent │ └── MDP │ │ ├── complete_files │ │ ├── em.0.mdp │ │ ├── em.1.mdp │ │ ├── em.10.mdp │ │ ├── em.11.mdp │ │ ├── em.12.mdp │ │ ├── em.13.mdp │ │ ├── em.2.mdp │ │ ├── em.3.mdp │ │ ├── em.4.mdp │ │ ├── em.5.mdp │ │ ├── em.6.mdp │ │ ├── em.7.mdp │ │ ├── em.8.mdp │ │ ├── em.9.mdp │ │ ├── nvt.0.mdp │ │ ├── nvt.1.mdp │ │ ├── nvt.10.mdp │ │ ├── nvt.11.mdp │ │ ├── nvt.12.mdp │ │ ├── nvt.13.mdp │ │ ├── nvt.2.mdp │ │ ├── nvt.3.mdp │ │ ├── nvt.4.mdp │ │ ├── nvt.5.mdp │ │ ├── nvt.6.mdp │ │ ├── nvt.7.mdp │ │ ├── nvt.8.mdp │ │ ├── nvt.9.mdp │ │ ├── prod.0.mdp │ │ ├── prod.1.mdp │ │ ├── prod.10.mdp │ │ ├── prod.11.mdp │ │ ├── prod.12.mdp │ │ ├── prod.13.mdp │ │ ├── prod.2.mdp │ │ ├── prod.3.mdp │ │ ├── prod.4.mdp │ │ ├── prod.5.mdp │ │ ├── prod.6.mdp │ │ ├── prod.7.mdp │ │ ├── prod.8.mdp │ │ └── prod.9.mdp │ │ ├── em.X.mdp │ │ ├── make_files.py │ │ ├── nvt.X.mdp │ │ └── prod.X.mdp ├── septop_complex │ ├── MDP_step1 │ │ ├── complete_files │ │ │ ├── em.0.mdp │ │ │ ├── em.1.mdp │ │ │ ├── em.10.mdp │ │ │ ├── em.11.mdp │ │ │ ├── em.2.mdp │ │ │ ├── em.3.mdp │ │ │ ├── em.4.mdp │ │ │ ├── em.5.mdp │ │ │ ├── em.6.mdp │ │ │ ├── em.7.mdp │ │ │ ├── em.8.mdp │ │ │ ├── em.9.mdp │ │ │ ├── nvt.0.mdp │ │ │ ├── nvt.1.mdp │ │ │ ├── nvt.10.mdp │ │ │ ├── nvt.11.mdp │ │ │ ├── nvt.2.mdp │ │ │ ├── nvt.3.mdp │ │ │ ├── nvt.4.mdp │ │ │ ├── nvt.5.mdp │ │ │ ├── nvt.6.mdp │ │ │ ├── nvt.7.mdp │ │ │ ├── nvt.8.mdp │ │ │ ├── nvt.9.mdp │ │ │ ├── prod.0.mdp │ │ │ ├── prod.1.mdp │ │ │ ├── prod.10.mdp │ │ │ ├── prod.11.mdp │ │ │ ├── prod.2.mdp │ │ │ ├── prod.3.mdp │ │ │ ├── prod.4.mdp │ │ │ ├── prod.5.mdp │ │ │ ├── prod.6.mdp │ │ │ ├── prod.7.mdp │ │ │ ├── prod.8.mdp │ │ │ └── prod.9.mdp │ │ ├── em.X.mdp │ │ ├── make_files.py │ │ ├── nvt.X.mdp │ │ └── prod.X.mdp │ └── MDP_step2 │ │ ├── complete_files │ │ ├── em.0.mdp │ │ ├── em.1.mdp │ │ ├── em.2.mdp │ │ ├── em.3.mdp │ │ ├── em.4.mdp │ │ ├── em.5.mdp │ │ ├── em.6.mdp │ │ ├── em.7.mdp │ │ ├── nvt.0.mdp │ │ ├── nvt.1.mdp │ │ ├── nvt.2.mdp │ │ ├── nvt.3.mdp │ │ ├── nvt.4.mdp │ │ ├── nvt.5.mdp │ │ ├── nvt.6.mdp │ │ ├── nvt.7.mdp │ │ ├── prod.0.mdp │ │ ├── prod.1.mdp │ │ ├── prod.2.mdp │ │ ├── prod.3.mdp │ │ ├── prod.4.mdp │ │ ├── prod.5.mdp │ │ ├── prod.6.mdp │ │ └── prod.7.mdp │ │ ├── em.X.mdp │ │ ├── make_files.py │ │ ├── nvt.X.mdp │ │ └── prod.X.mdp └── septop_solvent │ ├── MDP_step1 │ ├── complete_files │ │ ├── em.0.mdp │ │ ├── em.1.mdp │ │ ├── em.10.mdp │ │ ├── em.11.mdp │ │ ├── em.12.mdp │ │ ├── em.13.mdp │ │ ├── em.14.mdp │ │ ├── em.15.mdp │ │ ├── em.16.mdp │ │ ├── em.17.mdp │ │ ├── em.2.mdp │ │ ├── em.3.mdp │ │ ├── em.4.mdp │ │ ├── em.5.mdp │ │ ├── em.6.mdp │ │ ├── em.7.mdp │ │ ├── em.8.mdp │ │ ├── em.9.mdp │ │ ├── nvt.0.mdp │ │ ├── nvt.1.mdp │ │ ├── nvt.10.mdp │ │ ├── nvt.11.mdp │ │ ├── nvt.12.mdp │ │ ├── nvt.13.mdp │ │ ├── nvt.14.mdp │ │ ├── nvt.15.mdp │ │ ├── nvt.16.mdp │ │ ├── nvt.17.mdp │ │ ├── nvt.2.mdp │ │ ├── nvt.3.mdp │ │ ├── nvt.4.mdp │ │ ├── nvt.5.mdp │ │ ├── nvt.6.mdp │ │ ├── nvt.7.mdp │ │ ├── nvt.8.mdp │ │ ├── nvt.9.mdp │ │ ├── prod.0.mdp │ │ ├── prod.1.mdp │ │ ├── prod.10.mdp │ │ ├── prod.11.mdp │ │ ├── prod.12.mdp │ │ ├── prod.13.mdp │ │ ├── prod.14.mdp │ │ ├── prod.15.mdp │ │ ├── prod.16.mdp │ │ ├── prod.17.mdp │ │ ├── prod.2.mdp │ │ ├── prod.3.mdp │ │ ├── prod.4.mdp │ │ ├── prod.5.mdp │ │ ├── prod.6.mdp │ │ ├── prod.7.mdp │ │ ├── prod.8.mdp │ │ └── prod.9.mdp │ ├── em.X.mdp │ ├── make_files.py │ ├── nvt.X.mdp │ └── prod.X.mdp │ └── MDP_step2 │ ├── complete_files │ ├── em.0.mdp │ ├── em.1.mdp │ ├── em.2.mdp │ ├── em.3.mdp │ ├── em.4.mdp │ ├── em.5.mdp │ ├── em.6.mdp │ ├── em.7.mdp │ ├── em.8.mdp │ ├── em.9.mdp │ ├── nvt.0.mdp │ ├── nvt.1.mdp │ ├── nvt.2.mdp │ ├── nvt.3.mdp │ ├── nvt.4.mdp │ ├── nvt.5.mdp │ ├── nvt.6.mdp │ ├── nvt.7.mdp │ ├── nvt.8.mdp │ ├── nvt.9.mdp │ ├── prod.0.mdp │ ├── prod.1.mdp │ ├── prod.2.mdp │ ├── prod.3.mdp │ ├── prod.4.mdp │ ├── prod.5.mdp │ ├── prod.6.mdp │ ├── prod.7.mdp │ ├── prod.8.mdp │ └── prod.9.mdp │ ├── em.X.mdp │ ├── make_files.py │ ├── nvt.X.mdp │ └── prod.X.mdp ├── README.md ├── boresch_restraints.py ├── combine_coordinates.py ├── distance_solvent.py ├── environment.yml ├── example └── BACE │ ├── complex │ ├── lig_13 │ │ ├── complex.gro │ │ ├── complex.pdb │ │ ├── complex.top │ │ └── lig_13.mol2 │ └── lig_16 │ │ ├── complex.gro │ │ ├── complex.pdb │ │ ├── complex.top │ │ ├── complex_fit.gro │ │ ├── complex_fit.pdb │ │ └── lig_16.mol2 │ ├── setup_bace_input.ipynb │ └── solvent │ ├── lig_13 │ ├── solvent.gro │ └── solvent.top │ └── lig_16 │ ├── solvent.gro │ └── solvent.top ├── make_absolute_top_solvent.py ├── make_septop.py ├── prep_SepTop_complex.py ├── prep_SepTop_solvent.py ├── prep_solvent_absolute.py └── rot_bonds.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MobleyLab/SeparatedTopologies/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: 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