GMX Automatic Ligand Parameterization tutorial using Biobb

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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.

Code Snippets

baseCommand: acpype_params_gmx

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_chemistry:4.0.0--pyhdfd78af_1

inputs:
  input_path:
    label: Path to the input file
    doc: |-
      Path to the input file
      Type: string
      File type: input
      Accepted formats: pdb, mdl, mol2
      Example file: https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/data/acpype/acpype.params.mol2
    type: File
    format:
    - edam:format_1476
    - edam:format_3815
    - edam:format_3816
    inputBinding:
      position: 1
      prefix: --input_path

  output_path_gro:
    label: Path to the GRO output file
    doc: |-
      Path to the GRO output file
      Type: string
      File type: output
      Accepted formats: gro
      Example file: https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.gro
    type: string
    format:
    - edam:format_2033
    inputBinding:
      position: 2
      prefix: --output_path_gro
    default: system.gro

  output_path_itp:
    label: Path to the ITP output file
    doc: |-
      Path to the ITP output file
      Type: string
      File type: output
      Accepted formats: itp
      Example file: https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.itp
    type: string
    format:
    - edam:format_3883
    inputBinding:
      position: 3
      prefix: --output_path_itp
    default: system.itp

  output_path_top:
    label: Path to the TOP output file
    doc: |-
      Path to the TOP output file
      Type: string
      File type: output
      Accepted formats: top
      Example file: https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.top
    type: string
    format:
    - edam:format_3880
    inputBinding:
      position: 4
      prefix: --output_path_top
    default: system.top

  config:
    label: Advanced configuration options for biobb_chemistry AcpypeParamsGMX
    doc: |-
      Advanced configuration options for biobb_chemistry AcpypeParamsGMX. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_chemistry AcpypeParamsGMX documentation: https://biobb-chemistry.readthedocs.io/en/latest/acpype.html#module-acpype.acpype_params_gmx
    type: string?
    inputBinding:
      prefix: --config

CWL ACPYPE From line 11 of biobb_adapters/acpype_params_gmx.cwl

baseCommand: babel_minimize

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_chemistry:4.0.0--pyhdfd78af_1

inputs:
  input_path:
    label: Path to the input file
    doc: |-
      Path to the input file
      Type: string
      File type: input
      Accepted formats: pdb, mol2
      Example file: https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/data/babel/babel.minimize.pdb
    type: File
    format:
    - edam:format_1476
    - edam:format_3816
    inputBinding:
      position: 1
      prefix: --input_path

  output_path:
    label: Path to the output file
    doc: |-
      Path to the output file
      Type: string
      File type: output
      Accepted formats: pdb, mol2
      Example file: https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/babel/ref_babel.minimize.pdb
    type: string
    format:
    - edam:format_1476
    - edam:format_3816
    inputBinding:
      position: 2
      prefix: --output_path
    default: system.pdb

  config:
    label: Advanced configuration options for biobb_chemistry BabelMinimize
    doc: |-
      Advanced configuration options for biobb_chemistry BabelMinimize. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_chemistry BabelMinimize documentation: https://biobb-chemistry.readthedocs.io/en/latest/babelm.html#module-babelm.babel_minimize
    type: string?
    inputBinding:
      prefix: --config