Jupyter GMX Notebook Automatic Ligand Parameterization tutorial
Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)
This tutorial aims to illustrate the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Sulfasalazine protein (3-letter code SAS), used to treat rheumatoid arthritis, ulcerative colitis, and Crohn's disease.
OpenBabel and ACPype packages are used to add hydrogens, energetically minimize the structure, and generate parameters for the GROMACS package. With Generalized Amber Force Field (GAFF) forcefield and AM1-BCC charges.
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 4 (latest) Created 14th Apr 2023 at 08:51 by Genís Bayarri
Update to BioBB 4.0.*
Version 3 Created 15th Sep 2022 at 11:59 by Genís Bayarri
Update to BioBB 3.8.*. taken from Git commit 2a351bf
Version 2 Created 29th Jun 2021 at 08:40 by Robin Long
Updated to BioBB 3.6.0. Taken from Git commit 461262dae
Version 1 (earliest) Created 14th Sep 2020 at 11:01 by Robin Long
Initial Commit. Taken from Git commit c6cb736
Created: 14th Sep 2020 at 11:01
Last updated: 14th Apr 2023 at 08:53