Jupyter Notebook Amber Protein Ligand Complex MD Setup tutorial
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Download RO-CrateAMBER Protein MD Setup tutorials 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, step by step, using the BioExcel Building Blocks library (biobb) wrapping the Ambertools MD package.
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 6 (latest) Created 6th Aug 2025 at 13:14 by Genís Bayarri
Update to 5.1.*
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Version-6c3a0aff
Version 4 Created 26th Jul 2023 at 10:37 by Genís Bayarri
Fixed importlib_metadata bug
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Version-4
551b8dd
Version 3 Created 14th Apr 2023 at 09:35 by Genís Bayarri
Update to BioBB 4.0.*
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Version-3
121c8a7
Version 2 Created 15th Sep 2022 at 13:31 by Genís Bayarri
Update to BioBB 3.8.*. taken from Git commit faad0ab
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Version-2
49aff06
Version 1 (earliest) Created 30th Jun 2021 at 13:18 by Genís Bayarri
Initial commit. Taken from Git commit 5ae6892
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Version-1
837ff61
Creators and Submitter
Views: 8306 Downloads: 2839
Created: 30th Jun 2021 at 13:18
Last updated: 6th Aug 2025 at 13:15
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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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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 ...
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