Python Protein Ligand Complex MD Setup tutorial
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Protein 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).

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

SEEK ID: https://workflowhub.eu/workflows/281?version=1

DOI: 10.48546/workflowhub.workflow.281.1

Version History

Version 3 (latest) Created 14th Apr 2023 at 09:07 by Genís Bayarri

Update to BioBB 4.0.*

Frozen Version-3 f39cff9

Version 2 Created 22nd Nov 2022 at 10:00 by Genís Bayarri

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Frozen Version-2 6240e1a

Version 1 (earliest) Created 17th Mar 2022 at 09:57 by Genís Bayarri

Initial commit

Frozen Version-1 28bcb96

Creators and Submitter

Creators

Submitter

Genís Bayarri

Discussion Channels

BioExcel Workflows

Tutorial

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Citation

Bayarri, G., & Hospital, A. (2022). Python Protein Ligand Complex MD Setup tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.281.1

License

Apache License 2.0

Activity

Views: 2921 Downloads: 713

Created: 17th Mar 2022 at 09:57

Last updated: 14th Apr 2023 at 09:07

Python Protein Ligand Complex MD Setup tutorial Version 1 (earliest) Version 3 (latest) Version 2 Version 1 (earliest)