Protein 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, 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

Total size: 51.8 KB
help Creators and Submitter
Lowe, D., Bayarri, G., & Hospital, A. (2021). Protein MD Setup tutorial using BioExcel Building Blocks (biobb). WorkflowHub.

Views: 944   Downloads: 6

Created: 7th May 2021 at 14:51

Last updated: 8th Jul 2021 at 10:04

Last used: 22nd Jan 2022 at 17:23

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Version History

Version 2 (latest) Created 1st Jul 2021 at 15:51 by Douglas Lowe

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Open master d4040dc

Version 1 (earliest) 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

Frozen master 46c5b2e

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