Jupyter Notebook Protein Ligand Complex MD Setup tutorial
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Download RO-CrateProtein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb)
Based on the official GROMACS tutorial.
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).
Copyright & Licensing
This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).
- (c) 2015-2025 Barcelona Supercomputing Center
- (c) 2015-2025 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
Version History
Version 8 (latest) Created 6th Aug 2025 at 10:19 by Genís Bayarri
Update to BioBB 5.1.*
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Version-8925ba0a
Version 7 Created 4th Mar 2024 at 14:23 by Genís Bayarri
Update to BioBB 4.1.*
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Version-7
70dfb75
Version 6 Created 26th Jul 2023 at 10:21 by Genís Bayarri
Fixed importlib_metadata bug
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Version-6
3b0b8b7
Version 5 Created 14th Apr 2023 at 09:04 by Genís Bayarri
Update to BioBB 4.0.*
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Version-5
1a1f58d
Version 4 Created 15th Sep 2022 at 12:04 by Genís Bayarri
Update to BioBB 3.8.*. taken from Git commit 29a9ec9
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Version-4
99d4200
Version 3 Created 2nd Jul 2021 at 09:43 by Douglas Lowe
Updated to BioBB 3.6.0. Taken from Git commit 513b6af
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Version-3
9f15c63
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
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master14efaa7
Version 1 (earliest) Created 22nd Sep 2020 at 16:30 by Douglas Lowe
Initial Upload. Taken from Git commit b4eee4f
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master
877b1b7
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Views: 14000 Downloads: 4072
Created: 22nd Sep 2020 at 16:30
Last updated: 6th Aug 2025 at 10:22
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https://orcid.org/0000-0003-0513-0288
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.
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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/
Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation, and the possibility to inspect intermediate results with versatile graphical charts and data visualization is very helpful, especially in iterative processes, where parameters might be adjusted to a particular system of interest. This work ...
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