Workflow Type: Jupyter
Stable

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 4 (latest) 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
Citation
Bayarri, G., & Hospital, A. (2022). Jupyter Notebook Protein Ligand Complex MD Setup tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.56.4
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Views: 2768

Created: 22nd Sep 2020 at 16:30

Last updated: 17th Mar 2022 at 09:51

Last used: 6th Oct 2022 at 13:29

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