Workflow Type: Galaxy
Stable

Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)


This workflow must be run in biobb.usegalaxy.es. Please, click here to access.


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.

Steps

ID Name Description
0 Ligand biobb_io_ligand_ext
1 BabelAddHydrogens biobb_chemistry_babel_add_hydrogens_ext
2 BabelMinimize biobb_chemistry_babel_minimize_ext
3 AcpypeParamsGmx biobb_chemistry_acpype_params_gmx_ext

Outputs

ID Name Description Type
myligand.pdb myligand.pdb n/a
  • File
_anonymous_output_1 _anonymous_output_1 n/a
  • File
mybabel_minimize.pdb mybabel_minimize.pdb n/a
  • File
myacpype_params_gmx.itp myacpype_params_gmx.itp n/a
  • File
myacpype_params_gmx.top myacpype_params_gmx.top n/a
  • File
myacpype_params_gmx.gro myacpype_params_gmx.gro n/a
  • File

Version History

Version 3 (latest) Created 3rd May 2023 at 14:44 by Genís Bayarri

Update to BioBB 4.0.*


Frozen Version-3 30ea7b9

Version 2 Created 22nd Nov 2022 at 09:50 by Genís Bayarri

No revision comments

Frozen Version-2 548d9ff

Version 1 (earliest) Created 24th Mar 2022 at 14:09 by Genís Bayarri

Initial commit


Frozen Version-1 428c7cf
help Creators and Submitter
Citation
Hospital, A., & Bayarri, G. (2023). Galaxy GMX Automatic Ligand Parameterization tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.294.3
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Views: 2785

Created: 24th Mar 2022 at 14:09

Last updated: 3rd May 2023 at 14:44

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