Summary

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

Inputs

Parameters needed to configure the workflow:

• pdbCode: PDB code of the protein-ligand complex structure (e.g. 1AKI)

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