Jupyter Notebook Protein Ligand Complex MD Setup tutorial
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).
- (c) 2015-2023 Barcelona Supercomputing Center
- (c) 2015-2023 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
Version 5 (latest) Created 14th Apr 2023 at 09:04 by Genís Bayarri
Update to BioBB 4.0.*
Version 4 Created 15th Sep 2022 at 12:04 by Genís Bayarri
Update to BioBB 3.8.*. taken from Git commit 29a9ec9
Version 3 Created 2nd Jul 2021 at 09:43 by Douglas Lowe
Updated to BioBB 3.6.0. Taken from Git commit 513b6af
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
Version 1 (earliest) Created 22nd Sep 2020 at 16:30 by Douglas Lowe
Initial Upload. Taken from Git commit b4eee4f
Created: 22nd Sep 2020 at 16:30
Last updated: 14th Apr 2023 at 09:05