Jupyter Notebook GMX Notebook Automatic Ligand Parameterization tutorial

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Summary

Jupyter Notebook containing a tutorial 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.

Parameters

Inputs:

  • ligandCode: 3-letter code of the ligand structure (e.g. IBP)

  • mol_charge: Molecule net charge (e.g. -1)

  • pH: Acidity or alkalinity for the small molecule. Hydrogen atoms will be added according to this pH. (e.g. 7.4)

Outputs

  • IBPparams.gro: Structure of the parameterized ligand in gro (GROMACS) format.

  • IBPparams.top: Topology of the parameterized ligand, including a reference to the IBPparams.itp.

  • IBPparams.itp: Include Topology File (itp) of the parameterized ligand, including the parameters information: bonds, angles, dihedrals, etc.

Additional Resources

SEEK ID: https://workflowhub.eu/workflows/54?version=1

DOI: 10.48546/workflowhub.workflow.54.1

Version History

Version 6 (latest) Created 4th Mar 2024 at 14:20 by Genís Bayarri

Update to BioBB 4.1.*


Frozen Version-6 f2526d7

Version 5 Created 26th Jul 2023 at 10:20 by Genís Bayarri

Fixed importlib_metadata bug


Frozen Version-5 62173bf

Version 4 Created 14th Apr 2023 at 08:51 by Genís Bayarri

Update to BioBB 4.0.*


Frozen Version-4 a3814ff

Version 3 Created 15th Sep 2022 at 11:59 by Genís Bayarri

Update to BioBB 3.8.*. taken from Git commit 2a351bf


Frozen Version-3 0e1ae08

Version 2 Created 29th Jun 2021 at 08:40 by Robin Long

Updated to BioBB 3.6.0. Taken from Git commit 461262dae


Frozen Version-2 461262d

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., & Bayarri, G. (2021). Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.54.1
License
Apache License 2.0
Activity

Views: 6155   Downloads: 1395

Created: 14th Sep 2020 at 11:01

Last updated: 5th Mar 2024 at 09:40

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