Jupyter 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 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 2 (latest) Created 29th Jun 2021 at 08:40 by Robin Long

Updated to BioBB 3.6.0. Taken from Git commit 28ef9a0


Open master d734c74

Version 1 (earliest) Created 14th Sep 2020 at 11:01 by Robin Long

Initial Commit. Taken from Git commit c6cb736


Frozen master eff4a17
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Citation
Long, R., Lowe, D., Bayarri, G., & Hospital, A. (2021). Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.54.2
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Views: 1521   Downloads: 32

Created: 14th Sep 2020 at 11:01

Last updated: 17th Mar 2022 at 14:07

Last used: 26th Jun 2022 at 07:23

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