Workflow Type: Jupyter

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.

Version History

Version 3 (latest) Created 14th Apr 2023 at 09:35 by Genís Bayarri

Update to BioBB 4.0.*

Frozen 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

Frozen Version-2 49aff06

Version 1 (earliest) Created 30th Jun 2021 at 13:18 by Genís Bayarri

Initial commit. Taken from Git commit 5ae6892

Frozen Version-1 837ff61
help Creators and Submitter
Bayarri, G., & Hospital, A. (2021). Protein-ligand complex MD Setup tutorial using BioExcel Building Blocks (biobb) (jupyter notebook). WorkflowHub.

Views: 1714

Created: 30th Jun 2021 at 13:18

Last updated: 14th Apr 2023 at 09:36

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