Workflow Type: Jupyter

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.

Version History

Version 7 (latest) Created 4th Mar 2024 at 14:23 by Genís Bayarri

Update to BioBB 4.1.*

Frozen Version-7 70dfb75

Version 6 Created 26th Jul 2023 at 10:21 by Genís Bayarri

Fixed importlib_metadata bug

Frozen Version-6 3b0b8b7

Version 5 Created 14th Apr 2023 at 09:04 by Genís Bayarri

Update to BioBB 4.0.*

Frozen Version-5 1a1f58d

Version 4 Created 15th Sep 2022 at 12:04 by Genís Bayarri

Update to BioBB 3.8.*. taken from Git commit 29a9ec9

Frozen Version-4 99d4200

Version 3 Created 2nd Jul 2021 at 09:43 by Douglas Lowe

Updated to BioBB 3.6.0. Taken from Git commit 513b6af

Frozen Version-3 9f15c63

Version 2 Created 6th May 2021 at 16:40 by Douglas Lowe

Updated for GROMACS 2020.4 and BioExcel Building Blocks version 3.5. Taken from Git commit 7e89a16

Frozen master 14efaa7

Version 1 (earliest) Created 22nd Sep 2020 at 16:30 by Douglas Lowe

Initial Upload. Taken from Git commit b4eee4f

Frozen master 877b1b7
help Creators and Submitter
Bayarri, G., & Hospital, A. (2022). Jupyter Notebook Protein Ligand Complex MD Setup tutorial. WorkflowHub.

Views: 6701   Downloads: 849

Created: 22nd Sep 2020 at 16:30

Last updated: 14th Apr 2023 at 09:05

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