Jupyter Notebook GMX Notebook Automatic Ligand Parameterization tutorial
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Download RO-CrateAutomatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)
This tutorial aims to illustrate the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Sulfasalazine protein (3-letter code SAS), used to treat rheumatoid arthritis, ulcerative colitis, and Crohn's disease.
OpenBabel and ACPype packages are used to add hydrogens, energetically minimize the structure, and generate parameters for the GROMACS package. With Generalized Amber Force Field (GAFF) forcefield and AM1-BCC charges.
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 7 (latest) Created 6th Aug 2025 at 08:51 by Genís Bayarri
Update to BioBB 5.1.*
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Version-7264d24f
Version 6 Created 4th Mar 2024 at 14:20 by Genís Bayarri
Update to BioBB 4.1.*
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Version-6
f2526d7
Version 5 Created 26th Jul 2023 at 10:20 by Genís Bayarri
Fixed importlib_metadata bug
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Version-5
62173bf
Version 4 Created 14th Apr 2023 at 08:51 by Genís Bayarri
Update to BioBB 4.0.*
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Version-4
a3814ff
Version 3 Created 15th Sep 2022 at 11:59 by Genís Bayarri
Update to BioBB 3.8.*. taken from Git commit 2a351bf
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Version-3
0e1ae08
Version 2 Created 29th Jun 2021 at 08:40 by Robin Long
Updated to BioBB 3.6.0. Taken from Git commit 461262dae
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Version-2
461262d
Version 1 (earliest) Created 14th Sep 2020 at 11:01 by Robin Long
Initial Commit. Taken from Git commit c6cb736
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Creators and SubmitterViews: 10812 Downloads: 3498
Created: 14th Sep 2020 at 11:01
Last updated: 6th Aug 2025 at 08:54
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Teams: BioBB Building Blocks, UX trial team
Organizations: The University of Manchester
https://orcid.org/0000-0003-2249-645X
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/
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 ...
Selection of BioExcel Building Blocks (BioBB) Workflows intended for tutorials and training.
