Protein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb)
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 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.
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