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

Workflow Type: Jupyter


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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Views: 1123   Downloads: 20

Created: 22nd Sep 2020 at 16:30

Last updated: 8th Jul 2021 at 10:07

Last used: 15th Oct 2021 at 00:03

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Version History

Version 3 (latest) Created 2nd Jul 2021 at 09:43 by Douglas Lowe

Updated to BioBB 3.6.0. Taken from Git commit 513b6af

Version 2 Created 6th May 2021 at 16:40 by Douglas Lowe

Updated for GROMACS 2020.4 and BioExcel Building Blocks version 3.5. Taken from Git commit 7e89a16

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

Initial Upload. Taken from Git commit b4eee4f

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