Jupyter Notebook GMX Notebook Automatic Ligand Parameterization tutorial

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# 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](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)). * (c) 2015-2026 [Barcelona Supercomputing Center](https://www.bsc.es/) * (c) 2015-2026 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/) Licensed under the [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details. 

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