Protein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb) (jupyter notebook)
Version 1



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

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Created: 22nd Sep 2020 at 16:30

Last updated: 22nd Sep 2020 at 16:46

Last used: 17th Apr 2021 at 06:48

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Version 1 Created 22nd Sep 2020 at 16:30 by Douglas Lowe

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