├── LICENSE ├── README.md ├── docker ├── Dockerfile ├── README ├── assets │ └── cleanup.sh └── build.sh ├── enlighten2 ├── __init__.py ├── dynam.py ├── examples │ ├── 1btl_0rn │ │ ├── 1btl_0rn.pdb │ │ ├── sp15.ph11_params │ │ ├── sp15.ph11_run.sh │ │ └── sp20.ph7_run.sh │ └── 5ldg_it9 │ │ ├── 5ldg.pdb │ │ ├── NAP.frcmod │ │ ├── NAP.prepc │ │ └── run.sh ├── md_monitor.py ├── pdb_utils.py ├── prep.py ├── sander │ ├── heat.in │ ├── md.in │ ├── min.in │ ├── min_ibelly.in │ ├── minh.in │ ├── minh_ibelly.in │ ├── sa.in │ └── sa_ca.in ├── sanderflow.py ├── tleap │ ├── __init__.py │ ├── sphere.in │ └── sphere.py ├── utils.py └── wrappers.py ├── setup.py └── tests ├── __init__.py ├── test_files ├── full.pdb ├── only_atoms.pdb ├── pdb4amber_nonprot.pdb ├── propka.pka ├── reduce.pdb └── sphere.in ├── test_pdb_utils.py ├── test_utils.py └── test_wrappers.py /LICENSE: -------------------------------------------------------------------------------- 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