Protein MD Setup tutorial using BioExcel Building Blocks (biobb)
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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
Inputs
Parameters needed to configure the workflow:
- pdbCode: PDB code of the protein-ligand complex structure (e.g. 1AKI)
Outputs
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
Creators and SubmitterViews: 623 Downloads: 5
Created: 7th May 2021 at 14:51
Last updated: 8th Jul 2021 at 10:04
Last used: 16th Oct 2021 at 15:17
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Version 2 (latest) Created 1st Jul 2021 at 15:51 by Douglas Lowe
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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
Related items
Teams: BioBB Building Blocks
Organizations: The University of Manchester
https://orcid.org/0000-0002-1248-3594
BioExcel is the leading European Centre of Excellence for Computational Biomolecular Research. Established in 2015, the centre has grown into a major research and innovation hub for scientific computing. BioExcel develops some of the most popular applications for modelling and simulations of biomolecular systems. A broad range of additional pre-/post-processing tools are integrated with the core applications within user-friendly workflows and container solutions.
The software stack comes with ...
Teams: BioBB Building Blocks, BioExcel Best Practice Guides
Web page: https://bioexcel.eu/
The BioExcel Building Blocks (biobb) software library is a collection of Python wrappers on top of popular biomolecular simulation tools. This library offers a layer of interoperability between the wrapped tools, which make them compatible and prepared to be directly interconnected to build complex biomolecular workflows. The building blocks can be used in many different workflow systems, including Galaxy, CWL, Jupyter Notebook and PyCOMPSs – notably their ...
Space: BioExcel
Public web page: https://mmb.irbbarcelona.org/biobb/
Selection of BioExcel Building Blocks (BioBB) Workflows, across three workflow languages (jupyter notebooks, CWL, and Galaxy), demonstrating the use of BioBB tool descriptors for each of these systems.
Maintainers: Douglas Lowe, Stian Soiland-Reyes, Adam Hospital, Genís Bayarri, Pau Andrio
# items: 5
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Selection of BioExcel Building Blocks (BioBB) Workflows intended for tutorials and training.
