Workflow Type: Common Workflow Language
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.

Click and drag the diagram to pan, double click or use the controls to zoom.

Inputs

ID Name Description Type
step2_babel_minimize_input_path Input file Path to the input file.
  • File
step2_babel_minimize_output_path Output file Path to the output file.
  • string
step2_babel_minimize_config Config file Configuration file for biobb_chemistry.babel_minimize tool.
  • string
step3_acpype_params_gmx_output_path_gro Output file Path to the GRO output file.
  • string
step3_acpype_params_gmx_output_path_itp Output file Path to the ITP output file.
  • string
step3_acpype_params_gmx_output_path_top Output file Path to the TOP output file.
  • string
step3_acpype_params_gmx_config Config file Configuration file for biobb_chemistry.acpype_params_gmx tool.
  • string

Steps

ID Name Description
step2_babel_minimize babel_minimize Energetically minimize small molecules.
step3_acpype_params_gmx acpype_params_gmx Small molecule parameterization for GROMACS MD package.

Outputs

ID Name Description Type
step2_babel_minimize_out1 output_path Path to the output file.
  • File
step3_acpype_params_gmx_out1 output_path_gro Path to the GRO output file.
  • File
step3_acpype_params_gmx_out2 output_path_itp Path to the ITP output file.
  • File
step3_acpype_params_gmx_out3 output_path_top Path to the TOP output file.
  • File

Version History

Version 2 (latest) Created 6th Jun 2023 at 13:24 by Genís Bayarri

Updated workflow descriptors


Frozen Version-2 dda947f

Version 1 (earliest) Created 10th Jan 2022 at 10:39 by Genís Bayarri

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Frozen Version-1 f7acba5
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Citation
Hospital, A., & Bayarri, G. (2023). CWL GMX Automatic Ligand Parameterization tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.255.2
Activity

Views: 2280

Created: 10th Jan 2022 at 10:39

Last updated: 17th Mar 2022 at 14:06

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