Python Amber Protein MD Setup tutorial

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AMBER 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).

Licensed under the Apache License 2.0, see the file LICENSE for details.

SEEK ID: https://workflowhub.eu/workflows/283?version=4

DOI: 10.48546/workflowhub.workflow.283.4

Version History

Version 4 (latest) Created 6th Aug 2025 at 12:55 by Genís Bayarri

Update to 5.1.*


Frozen Version-4 3f18047

Version 3 Created 14th Apr 2023 at 09:32 by Genís Bayarri

No revision comments

Frozen Version-3 5b00d82

Version 2 Created 23rd Nov 2022 at 08:41 by Genís Bayarri

Update to BioBB 3.8.*


Frozen Version-2 31c1fa5

Version 1 (earliest) Created 17th Mar 2022 at 10:27 by Genís Bayarri

Initial commit


Frozen Version-1 9427bff
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Citation
Hospital, A., & Bayarri, G. (2025). Python Amber Protein MD Setup tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.283.4
License
Apache License 2.0 (Apache-2.0)
Activity

Views: 5534   Downloads: 1651

Created: 17th Mar 2022 at 10:27

Last updated: 6th Aug 2025 at 12:57

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