Workflow Type: Python
Stable

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 3 (latest) Created 22nd Nov 2022 at 09:52 by Genís Bayarri

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Frozen Version-3 213963a

Version 2 Created 24th Mar 2022 at 14:17 by Genís Bayarri

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Frozen Version-2 224f422

Version 1 (earliest) Created 17th Mar 2022 at 09:41 by Genís Bayarri

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Frozen Version-1 56f91f4
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Citation
Hospital, A., & Bayarri, G. (2022). Python GMX Automatic Ligand Parameterization tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.280.3
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Views: 748

Created: 17th Mar 2022 at 09:41

Last updated: 17th Mar 2022 at 14:06

Last used: 8th Dec 2022 at 16:01

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