Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)

Workflow Type: Jupyter
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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

help Creators and Submitter
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
Activity

Views: 762   Downloads: 29

Created: 14th Sep 2020 at 11:01

Last updated: 8th Jul 2021 at 10:10

Last used: 15th Oct 2021 at 19:43

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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

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

Initial Commit. Taken from Git commit c6cb736

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