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
Licensed under the Apache License 2.0, see the file LICENSE for details.
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Created: 14th Sep 2020 at 11:01
Last updated: 17th Mar 2022 at 14:07
Last used: 26th Jun 2022 at 07:23