Protein MD Setup tutorial using BioExcel Building Blocks (biobb)
This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).
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, plotly, and simpletraj. Environment can be setup using the included environment.yml file.
Parameters needed to configure the workflow:
- pdbCode: PDB code of the protein-ligand complex structure (e.g. 1AKI)
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