CWL GMX Automatic Ligand Parameterization tutorial
Version 1

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.

Inputs

ID Name Description Type
step2_babel_minimize_config n/a n/a
  • string
step2_babel_minimize_input_path n/a n/a
  • File
step2_babel_minimize_output_path n/a n/a
  • string
step3_acpype_params_gmx_config n/a n/a
  • string
step3_acpype_params_gmx_output_path_gro n/a n/a
  • string
step3_acpype_params_gmx_output_path_itp n/a n/a
  • string
step3_acpype_params_gmx_output_path_top n/a n/a
  • string

Steps

ID Name Description
step2_babel_minimize BabelMinimize Energetically minimize small molecules.
step3_acpype_params_gmx AcpypeParamsGMX 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 1 (earliest) Created 10th Jan 2022 at 10:39 by Genís Bayarri

Fetched ligand.pdb from URL


Open master f7acba5
help Creators and Submitter
Citation
Bayarri, G., & Hospital, A. (2022). Automatic Ligand parameterization for GROMACS. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.255.1
Activity

Views: 683   Downloads: 2

Created: 10th Jan 2022 at 10:39

Last updated: 17th Mar 2022 at 14:06

Last used: 29th Nov 2022 at 03:45

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