├── .gitignore ├── LICENSE ├── README.md ├── channel_analysis.py ├── contacts.py ├── diversemdselect.py ├── mdrmsdplot.py ├── mstripit ├── pdb_util.py ├── prepareamber.py ├── reparm_ligand.py ├── rmsdtofirst.py ├── rmsf.py ├── simplepdb.py ├── splittraj.py ├── tests ├── 3EML.pdb ├── LIG_h.pdb ├── LIG_noh.pdb ├── LIGreceptor.pdb ├── LIGreceptor_fixed.pdb ├── LIGreceptor_number.pdb ├── ZMA.pdb ├── chignolin.pdb ├── env.py ├── env.pyc ├── receptor.pdb └── test_simplepdb.py ├── trajalign.py └── waters.py /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | tags 3 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dkoes/md-scripts/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: 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