Research Object Crate for Protein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb) (jupyter notebook)

# Summary This tutorial aims to illustrate the process of setting up a simulation system containing a protein in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the T4 lysozyme L99A/M102Q protein (PDB code 3HTB), in complex with the 2-propylphenol small molecule (3-letter Code JZ4). Workflow engine is a jupyter notebook. It can be run in binder, following the link given, or locally. Auxiliar libraries used are: nb\_conda_kernels, nglview, ipywidgets, os, plotly, and simpletraj. Environment can be setup using the included environment.yml file. # Parameters ## Inputs Parameters needed to configure the workflow: * **pdbCode**: PDB code of the protein-ligand complex structure (e.g. 3HTB) * **ligandCode**: Small molecule 3-letter code for the ligand structure (e.g. JZ4) * **mol\_charge**: Charge of the small molecule, needed to add hydrogen atoms. ## Outputs Output files generated (named according to the input parameters given above): * **output\_md\_gro**: final structure of the MD setup protocol * **output\_md\_trr**: final trajectory of the MD setup protocol * **output\_md\_cpt**: final checkpoint file * **output\_gppmd\_tpr**: final tpr file * **output\_genion\_top\_zip**: final topology of the MD system

Author

Genís Bayarri, Adam Hospital

License

Apache-2.0

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