Protein 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, 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

help Creators and Submitter
Lowe, D., & Bayarri, G. (2021). Protein MD Setup tutorial using BioExcel Building Blocks (biobb) (jupyter notebook). WorkflowHub.

Views: 221   Downloads: 2

Created: 7th May 2021 at 14:51

Last updated: 13th May 2021 at 09:14

Last used: 24th Jun 2021 at 23:30

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Version 1 Created 7th May 2021 at 14:51 by Douglas Lowe

Uses GROMACS 2020.4 and BioExcel Building Blocks version 3.5. Taken from Git commit a81b483

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