CWL Protein Ligand Complex MD Setup tutorial using Biobb

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Protein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb)

Based on the official GROMACS tutorial .

This tutorial aims to illustrate the process of setting up a simulation system containing a protein in complex with a ligand , step by step, using the BioExcel Building Blocks library (biobb) . The particular example used is the T4 lysozyme L99A/M102Q protein (PDB code 3HTB), in complex with the 2-propylphenol small molecule (3-letter Code JZ4).

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

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baseCommand: append_ligand

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

inputs:
  input_top_zip_path:
    label: Path the input topology TOP and ITP files zipball
    doc: |-
      Path the input topology TOP and ITP files zipball
      Type: string
      File type: input
      Accepted formats: zip
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs_extra/ndx2resttop.zip
    type: File
    format:
    - edam:format_3987
    inputBinding:
      position: 1
      prefix: --input_top_zip_path

  input_itp_path:
    label: Path to the ligand ITP file to be inserted in the topology
    doc: |-
      Path to the ligand ITP file to be inserted in the topology
      Type: string
      File type: input
      Accepted formats: itp
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs_extra/pep_ligand.itp
    type: File
    format:
    - edam:format_3883
    inputBinding:
      position: 2
      prefix: --input_itp_path

  output_top_zip_path:
    label: Path/Name the output topology TOP and ITP files zipball
    doc: |-
      Path/Name the output topology TOP and ITP files zipball
      Type: string
      File type: output
      Accepted formats: zip
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs_extra/ref_appendligand.zip
    type: string
    format:
    - edam:format_3987
    inputBinding:
      position: 3
      prefix: --output_top_zip_path
    default: system.zip

  input_posres_itp_path:
    label: Path to the position restriction ITP file
    doc: |-
      Path to the position restriction ITP file
      Type: string
      File type: input
      Accepted formats: itp
      Example file: null
    type: File?
    format:
    - edam:format_3883
    inputBinding:
      prefix: --input_posres_itp_path

  config:
    label: Advanced configuration options for biobb_gromacs AppendLigand
    doc: |-
      Advanced configuration options for biobb_gromacs AppendLigand. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_gromacs AppendLigand documentation: https://biobb-gromacs.readthedocs.io/en/latest/gromacs_extra.html#gromacs-extra-append-ligand-module
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_gromacs From line 11 of biobb_adapters/append_ligand.cwl 
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baseCommand: cat_pdb

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_structure_utils:4.0.0--pyhdfd78af_0

inputs:
  input_structure1:
    label: Input structure 1 file path
    doc: |-
      Input structure 1 file path
      Type: string
      File type: input
      Accepted formats: pdb, pdbqt
      Example file: https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/cat_protein.pdb
    type: File
    format:
    - edam:format_1476
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_structure1

  input_structure2:
    label: Input structure 2 file path
    doc: |-
      Input structure 2 file path
      Type: string
      File type: input
      Accepted formats: pdb, pdbqt
      Example file: https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/cat_ligand.pdb
    type: File
    format:
    - edam:format_1476
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --input_structure2

  output_structure_path:
    label: Output protein file path
    doc: |-
      Output protein file path
      Type: string
      File type: output
      Accepted formats: pdb, pdbqt
      Example file: https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_cat_pdb.pdb
    type: string
    format:
    - edam:format_1476
    - edam:format_1476
    inputBinding:
      position: 3
      prefix: --output_structure_path
    default: system.pdb

  config:
    label: Advanced configuration options for biobb_structure_utils CatPDB
    doc: |-
      Advanced configuration options for biobb_structure_utils CatPDB. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_structure_utils CatPDB documentation: https://biobb-structure-utils.readthedocs.io/en/latest/utils.html#module-utils.cat_pdb
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_structure_utils From line 11 of biobb_adapters/cat_pdb.cwl 
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baseCommand: editconf

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

inputs:
  input_gro_path:
    label: Path to the input GRO file
    doc: |-
      Path to the input GRO file
      Type: string
      File type: input
      Accepted formats: gro, pdb
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/editconf.gro
    type: File
    format:
    - edam:format_2033
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_gro_path

  output_gro_path:
    label: Path to the output GRO file
    doc: |-
      Path to the output GRO file
      Type: string
      File type: output
      Accepted formats: pdb, gro
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_editconf.gro
    type: string
    format:
    - edam:format_1476
    - edam:format_2033
    inputBinding:
      position: 2
      prefix: --output_gro_path
    default: system.pdb

  config:
    label: Advanced configuration options for biobb_gromacs Editconf
    doc: |-
      Advanced configuration options for biobb_gromacs Editconf. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_gromacs Editconf documentation: https://biobb-gromacs.readthedocs.io/en/latest/gromacs.html#module-gromacs.editconf
    type: string?
    inputBinding:
      prefix: --config
CWL editconf From line 11 of biobb_adapters/editconf.cwl 
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baseCommand: extract_molecule

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_structure_utils:4.0.0--pyhdfd78af_0

inputs:
  input_structure_path:
    label: Input structure file path
    doc: |-
      Input structure file path
      Type: string
      File type: input
      Accepted formats: pdb, pdbqt
      Example file: https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/extract_molecule.pdb
    type: File
    format:
    - edam:format_1476
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_structure_path

  output_molecule_path:
    label: Output molecule file path
    doc: |-
      Output molecule file path
      Type: string
      File type: output
      Accepted formats: pdb, pdbqt
      Example file: https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_extract_molecule.pdb
    type: string
    format:
    - edam:format_1476
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --output_molecule_path
    default: system.pdb

  config:
    label: Advanced configuration options for biobb_structure_utils ExtractMolecule
    doc: |-
      Advanced configuration options for biobb_structure_utils ExtractMolecule. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_structure_utils ExtractMolecule documentation: https://biobb-structure-utils.readthedocs.io/en/latest/utils.html#module-utils.extract_molecule
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_structure_utils From line 12 of biobb_adapters/extract_molecule.cwl 
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baseCommand: fix_side_chain

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_model:4.0.0--pyhdfd78af_0

inputs:
  input_pdb_path:
    label: Input PDB file path
    doc: |-
      Input PDB file path
      Type: string
      File type: input
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_model/raw/master/biobb_model/test/data/model/2ki5.pdb
    type: File
    format:
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_pdb_path

  output_pdb_path:
    label: Output PDB file path
    doc: |-
      Output PDB file path
      Type: string
      File type: output
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_model/raw/master/biobb_model/test/reference/model/output_pdb_path.pdb
    type: string
    format:
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --output_pdb_path
    default: system.pdb

  config:
    label: Advanced configuration options for biobb_model FixSideChain
    doc: |-
      Advanced configuration options for biobb_model FixSideChain. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_model FixSideChain documentation: https://biobb-model.readthedocs.io/en/latest/model.html#module-model.fix_side_chain
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_model From line 11 of biobb_adapters/fix_side_chain.cwl 
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baseCommand: genion

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

inputs:
  input_tpr_path:
    label: Path to the input portable run input TPR file
    doc: |-
      Path to the input portable run input TPR file
      Type: string
      File type: input
      Accepted formats: tpr
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/genion.tpr
    type: File
    format:
    - edam:format_2333
    inputBinding:
      position: 1
      prefix: --input_tpr_path

  output_gro_path:
    label: Path to the input structure GRO file
    doc: |-
      Path to the input structure GRO file
      Type: string
      File type: output
      Accepted formats: gro
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_genion.gro
    type: string
    format:
    - edam:format_2033
    inputBinding:
      position: 2
      prefix: --output_gro_path
    default: system.gro

  input_top_zip_path:
    label: Path the input TOP topology in zip format
    doc: |-
      Path the input TOP topology in zip format
      Type: string
      File type: input
      Accepted formats: zip
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/genion.zip
    type: File
    format:
    - edam:format_3987
    inputBinding:
      position: 3
      prefix: --input_top_zip_path

  output_top_zip_path:
    label: Path the output topology TOP and ITP files zipball
    doc: |-
      Path the output topology TOP and ITP files zipball
      Type: string
      File type: output
      Accepted formats: zip
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_genion.zip
    type: string
    format:
    - edam:format_3987
    inputBinding:
      position: 4
      prefix: --output_top_zip_path
    default: system.zip

  input_ndx_path:
    label: Path to the input index NDX file
    doc: |-
      Path to the input index NDX file
      Type: string
      File type: input
      Accepted formats: ndx
      Example file: null
    type: File?
    format:
    - edam:format_2033
    inputBinding:
      prefix: --input_ndx_path

  config:
    label: Advanced configuration options for biobb_gromacs Genion
    doc: |-
      Advanced configuration options for biobb_gromacs Genion. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_gromacs Genion documentation: https://biobb-gromacs.readthedocs.io/en/latest/gromacs.html#module-gromacs.genion
    type: string?
    inputBinding:
      prefix: --config
CWL genion From line 11 of biobb_adapters/genion.cwl 
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baseCommand: genrestr

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

inputs:
  input_structure_path:
    label: Path to the input structure PDB, GRO or TPR format
    doc: |-
      Path to the input structure PDB, GRO or TPR format
      Type: string
      File type: input
      Accepted formats: pdb, gro, tpr
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/genrestr.gro
    type: File
    format:
    - edam:format_1476
    - edam:format_2033
    - edam:format_2333
    inputBinding:
      position: 1
      prefix: --input_structure_path

  output_itp_path:
    label: Path the output ITP topology file with restrains
    doc: |-
      Path the output ITP topology file with restrains
      Type: string
      File type: output
      Accepted formats: itp
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_genrestr.itp
    type: string
    format:
    - edam:format_3883
    inputBinding:
      position: 2
      prefix: --output_itp_path
    default: system.itp

  input_ndx_path:
    label: Path to the input GROMACS index file, NDX format
    doc: |-
      Path to the input GROMACS index file, NDX format
      Type: string
      File type: input
      Accepted formats: ndx
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/genrestr.ndx
    type: File?
    format:
    - edam:format_2033
    inputBinding:
      prefix: --input_ndx_path

  config:
    label: Advanced configuration options for biobb_gromacs Genrestr
    doc: |-
      Advanced configuration options for biobb_gromacs Genrestr. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_gromacs Genrestr documentation: https://biobb-gromacs.readthedocs.io/en/latest/gromacs.html#module-gromacs.genrestr
    type: string?
    inputBinding:
      prefix: --config
CWL Gromacs From line 11 of biobb_adapters/genrestr.cwl 
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baseCommand: gmx_energy

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_analysis:4.0.1--pyhdfd78af_0

inputs:
  input_energy_path:
    label: Path to the input EDR file
    doc: |-
      Path to the input EDR file
      Type: string
      File type: input
      Accepted formats: edr
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/energy.edr
    type: File
    format:
    - edam:format_2330
    inputBinding:
      position: 1
      prefix: --input_energy_path

  output_xvg_path:
    label: Path to the XVG output file
    doc: |-
      Path to the XVG output file
      Type: string
      File type: output
      Accepted formats: xvg
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_energy.xvg
    type: string
    format:
    - edam:format_2030
    inputBinding:
      position: 2
      prefix: --output_xvg_path
    default: system.xvg

  config:
    label: Advanced configuration options for biobb_analysis GMXEnergy
    doc: |-
      Advanced configuration options for biobb_analysis GMXEnergy. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_analysis GMXEnergy documentation: https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.gmx_energy
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_analysis gmx energy From line 12 of biobb_adapters/gmx_energy.cwl 
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baseCommand: gmx_image

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_analysis:4.0.1--pyhdfd78af_0

inputs:
  input_traj_path:
    label: Path to the GROMACS trajectory file
    doc: |-
      Path to the GROMACS trajectory file
      Type: string
      File type: input
      Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/trajectory.trr
    type: File
    format:
    - edam:format_3875
    - edam:format_3910
    - edam:format_2333
    - edam:format_2033
    - edam:format_2033
    - edam:format_1476
    - edam:format_3876
    inputBinding:
      position: 1
      prefix: --input_traj_path

  input_top_path:
    label: Path to the GROMACS input topology file
    doc: |-
      Path to the GROMACS input topology file
      Type: string
      File type: input
      Accepted formats: tpr, gro, g96, pdb, brk, ent
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/topology.tpr
    type: File
    format:
    - edam:format_2333
    - edam:format_2033
    - edam:format_2033
    - edam:format_1476
    - edam:format_2033
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --input_top_path

  output_traj_path:
    label: Path to the output file
    doc: |-
      Path to the output file
      Type: string
      File type: output
      Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_image.xtc
    type: string
    format:
    - edam:format_3875
    - edam:format_3910
    - edam:format_2333
    - edam:format_2033
    - edam:format_2033
    - edam:format_1476
    - edam:format_3876
    inputBinding:
      position: 3
      prefix: --output_traj_path
    default: system.xtc

  input_index_path:
    label: Path to the GROMACS index file
    doc: |-
      Path to the GROMACS index file
      Type: string
      File type: input
      Accepted formats: ndx
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/index.ndx
    type: File?
    format:
    - edam:format_2033
    inputBinding:
      prefix: --input_index_path

  config:
    label: Advanced configuration options for biobb_analysis GMXImage
    doc: |-
      Advanced configuration options for biobb_analysis GMXImage. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_analysis GMXImage documentation: https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.gmx_image
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_analysis Gromacs From line 12 of biobb_adapters/gmx_image.cwl 
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baseCommand: gmx_rgyr

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_analysis:4.0.1--pyhdfd78af_0

inputs:
  input_structure_path:
    label: Path to the input structure file
    doc: |-
      Path to the input structure file
      Type: string
      File type: input
      Accepted formats: tpr, gro, g96, pdb, brk, ent
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/topology.tpr
    type: File
    format:
    - edam:format_2333
    - edam:format_2033
    - edam:format_2033
    - edam:format_1476
    - edam:format_2033
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_structure_path

  input_traj_path:
    label: Path to the GROMACS trajectory file
    doc: |-
      Path to the GROMACS trajectory file
      Type: string
      File type: input
      Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/trajectory.trr
    type: File
    format:
    - edam:format_3875
    - edam:format_3910
    - edam:format_2333
    - edam:format_2033
    - edam:format_2033
    - edam:format_1476
    - edam:format_3876
    inputBinding:
      position: 2
      prefix: --input_traj_path

  output_xvg_path:
    label: Path to the XVG output file
    doc: |-
      Path to the XVG output file
      Type: string
      File type: output
      Accepted formats: xvg
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_rgyr.xvg
    type: string
    format:
    - edam:format_2030
    inputBinding:
      position: 3
      prefix: --output_xvg_path
    default: system.xvg

  input_index_path:
    label: Path to the GROMACS index file
    doc: |-
      Path to the GROMACS index file
      Type: string
      File type: input
      Accepted formats: ndx
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/index.ndx
    type: File?
    format:
    - edam:format_2033
    inputBinding:
      prefix: --input_index_path

  config:
    label: Advanced configuration options for biobb_analysis GMXRgyr
    doc: |-
      Advanced configuration options for biobb_analysis GMXRgyr. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_analysis GMXRgyr documentation: https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.gmx_rgyr
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_analysis Gromacs From line 14 of biobb_adapters/gmx_rgyr.cwl 
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baseCommand: gmx_rms

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_analysis:4.0.1--pyhdfd78af_0

inputs:
  input_structure_path:
    label: Path to the input structure file
    doc: |-
      Path to the input structure file
      Type: string
      File type: input
      Accepted formats: tpr, gro, g96, pdb, brk, ent
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/topology.tpr
    type: File
    format:
    - edam:format_2333
    - edam:format_2033
    - edam:format_2033
    - edam:format_1476
    - edam:format_2033
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_structure_path

  input_traj_path:
    label: Path to the GROMACS trajectory file
    doc: |-
      Path to the GROMACS trajectory file
      Type: string
      File type: input
      Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/trajectory.trr
    type: File
    format:
    - edam:format_3875
    - edam:format_3910
    - edam:format_2333
    - edam:format_2033
    - edam:format_2033
    - edam:format_1476
    - edam:format_3876
    inputBinding:
      position: 2
      prefix: --input_traj_path

  output_xvg_path:
    label: Path to the XVG output file
    doc: |-
      Path to the XVG output file
      Type: string
      File type: output
      Accepted formats: xvg
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_rms.xvg
    type: string
    format:
    - edam:format_2030
    inputBinding:
      position: 3
      prefix: --output_xvg_path
    default: system.xvg

  input_index_path:
    label: Path to the GROMACS index file
    doc: |-
      Path to the GROMACS index file
      Type: string
      File type: input
      Accepted formats: ndx
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/index.ndx
    type: File?
    format:
    - edam:format_2033
    inputBinding:
      prefix: --input_index_path

  config:
    label: Advanced configuration options for biobb_analysis GMXRms
    doc: |-
      Advanced configuration options for biobb_analysis GMXRms. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_analysis GMXRms documentation: https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.gmx_rms
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_analysis Gromacs From line 12 of biobb_adapters/gmx_rms.cwl 
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baseCommand: gmx_trjconv_str

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_analysis:4.0.1--pyhdfd78af_0

inputs:
  input_structure_path:
    label: Path to the input structure file
    doc: |-
      Path to the input structure file
      Type: string
      File type: input
      Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/trajectory.trr
    type: File
    format:
    - edam:format_3875
    - edam:format_3910
    - edam:format_2333
    - edam:format_2033
    - edam:format_2033
    - edam:format_1476
    - edam:format_3876
    inputBinding:
      position: 1
      prefix: --input_structure_path

  input_top_path:
    label: Path to the GROMACS input topology file
    doc: |-
      Path to the GROMACS input topology file
      Type: string
      File type: input
      Accepted formats: tpr, gro, g96, pdb, brk, ent
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/topology.tpr
    type: File
    format:
    - edam:format_2333
    - edam:format_2033
    - edam:format_2033
    - edam:format_1476
    - edam:format_2033
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --input_top_path

  output_str_path:
    label: Path to the output file
    doc: |-
      Path to the output file
      Type: string
      File type: output
      Accepted formats: pdb, xtc, trr, cpt, gro, g96, tng
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_trjconv.str.pdb
    type: string
    format:
    - edam:format_1476
    - edam:format_3875
    - edam:format_3910
    - edam:format_2333
    - edam:format_2033
    - edam:format_2033
    - edam:format_3876
    inputBinding:
      position: 3
      prefix: --output_str_path
    default: system.pdb

  input_index_path:
    label: Path to the GROMACS index file
    doc: |-
      Path to the GROMACS index file
      Type: string
      File type: input
      Accepted formats: ndx
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/index.ndx
    type: File?
    format:
    - edam:format_2033
    inputBinding:
      prefix: --input_index_path

  config:
    label: Advanced configuration options for biobb_analysis GMXTrjConvStr
    doc: |-
      Advanced configuration options for biobb_analysis GMXTrjConvStr. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_analysis GMXTrjConvStr documentation: https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.gmx_trjconv_str
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_analysis Gromacs From line 12 of biobb_adapters/gmx_trjconv_str.cwl 
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baseCommand: grompp

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

inputs:
  input_gro_path:
    label: Path to the input GROMACS structure GRO file
    doc: |-
      Path to the input GROMACS structure GRO file
      Type: string
      File type: input
      Accepted formats: gro
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/grompp.gro
    type: File
    format:
    - edam:format_2033
    inputBinding:
      position: 1
      prefix: --input_gro_path

  input_top_zip_path:
    label: Path to the input GROMACS topology TOP and ITP files in zip format
    doc: |-
      Path to the input GROMACS topology TOP and ITP files in zip format
      Type: string
      File type: input
      Accepted formats: zip
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/grompp.zip
    type: File
    format:
    - edam:format_3987
    inputBinding:
      position: 2
      prefix: --input_top_zip_path

  output_tpr_path:
    label: Path to the output portable binary run file TPR
    doc: |-
      Path to the output portable binary run file TPR
      Type: string
      File type: output
      Accepted formats: tpr
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_grompp.tpr
    type: string
    format:
    - edam:format_2333
    inputBinding:
      position: 3
      prefix: --output_tpr_path
    default: system.tpr

  input_cpt_path:
    label: Path to the input GROMACS checkpoint file CPT
    doc: |-
      Path to the input GROMACS checkpoint file CPT
      Type: string
      File type: input
      Accepted formats: cpt
      Example file: null
    type: File?
    format:
    - edam:format_2333
    inputBinding:
      prefix: --input_cpt_path

  input_ndx_path:
    label: Path to the input GROMACS index files NDX
    doc: |-
      Path to the input GROMACS index files NDX
      Type: string
      File type: input
      Accepted formats: ndx
      Example file: null
    type: File?
    format:
    - edam:format_2033
    inputBinding:
      prefix: --input_ndx_path

  input_mdp_path:
    label: Path to the input GROMACS MDP file
    doc: |-
      Path to the input GROMACS MDP file
      Type: string
      File type: input
      Accepted formats: mdp
      Example file: null
    type: File?
    format:
    - edam:format_2330
    inputBinding:
      prefix: --input_mdp_path

  config:
    label: Advanced configuration options for biobb_gromacs Grompp
    doc: |-
      Advanced configuration options for biobb_gromacs Grompp. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_gromacs Grompp documentation: https://biobb-gromacs.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp
    type: string?
    inputBinding:
      prefix: --config
CWL Gromacs From line 11 of biobb_adapters/grompp.cwl 
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baseCommand: make_ndx

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

inputs:
  input_structure_path:
    label: Path to the input GRO/PDB/TPR file
    doc: |-
      Path to the input GRO/PDB/TPR file
      Type: string
      File type: input
      Accepted formats: gro, pdb, tpr
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/make_ndx.tpr
    type: File
    format:
    - edam:format_2033
    - edam:format_1476
    - edam:format_2333
    inputBinding:
      position: 1
      prefix: --input_structure_path

  output_ndx_path:
    label: Path to the output index NDX file
    doc: |-
      Path to the output index NDX file
      Type: string
      File type: output
      Accepted formats: ndx
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_make_ndx.ndx
    type: string
    format:
    - edam:format_2033
    inputBinding:
      position: 2
      prefix: --output_ndx_path
    default: system.ndx

  input_ndx_path:
    label: Path to the input index NDX file
    doc: |-
      Path to the input index NDX file
      Type: string
      File type: input
      Accepted formats: ndx
      Example file: null
    type: File?
    format:
    - edam:format_2033
    inputBinding:
      prefix: --input_ndx_path

  config:
    label: Advanced configuration options for biobb_gromacs MakeNdx
    doc: |-
      Advanced configuration options for biobb_gromacs MakeNdx. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_gromacs MakeNdx documentation: https://biobb-gromacs.readthedocs.io/en/latest/gromacs.html#module-gromacs.make_ndx
    type: string?
    inputBinding:
      prefix: --config
CWL From line 11 of biobb_adapters/make_ndx.cwl 
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baseCommand: mdrun

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

inputs:
  input_tpr_path:
    label: Path to the portable binary run input file TPR
    doc: |-
      Path to the portable binary run input file TPR
      Type: string
      File type: input
      Accepted formats: tpr
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/mdrun.tpr
    type: File
    format:
    - edam:format_2333
    inputBinding:
      position: 1
      prefix: --input_tpr_path

  output_gro_path:
    label: Path to the output GROMACS structure GRO file
    doc: |-
      Path to the output GROMACS structure GRO file
      Type: string
      File type: output
      Accepted formats: gro
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_mdrun.gro
    type: string
    format:
    - edam:format_2033
    inputBinding:
      position: 2
      prefix: --output_gro_path
    default: system.gro

  output_edr_path:
    label: Path to the output GROMACS portable energy file EDR
    doc: |-
      Path to the output GROMACS portable energy file EDR
      Type: string
      File type: output
      Accepted formats: edr
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_mdrun.edr
    type: string
    format:
    - edam:format_2330
    inputBinding:
      position: 3
      prefix: --output_edr_path
    default: system.edr

  output_log_path:
    label: Path to the output GROMACS trajectory log file LOG
    doc: |-
      Path to the output GROMACS trajectory log file LOG
      Type: string
      File type: output
      Accepted formats: log
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_mdrun.log
    type: string
    format:
    - edam:format_2330
    inputBinding:
      position: 4
      prefix: --output_log_path
    default: system.log

  output_trr_path:
    label: Path to the GROMACS uncompressed raw trajectory file TRR
    doc: |-
      Path to the GROMACS uncompressed raw trajectory file TRR
      Type: string
      File type: output
      Accepted formats: trr
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_mdrun.trr
    type: string
    format:
    - edam:format_3910
    inputBinding:
      prefix: --output_trr_path
    default: system.trr

  input_cpt_path:
    label: Path to the input GROMACS checkpoint file CPT
    doc: |-
      Path to the input GROMACS checkpoint file CPT
      Type: string
      File type: input
      Accepted formats: cpt
      Example file: null
    type: File?
    format:
    - edam:format_2333
    inputBinding:
      prefix: --input_cpt_path

  output_xtc_path:
    label: Path to the GROMACS compressed trajectory file XTC
    doc: |-
      Path to the GROMACS compressed trajectory file XTC
      Type: string
      File type: output
      Accepted formats: xtc
      Example file: null
    type: string
    format:
    - edam:format_3875
    inputBinding:
      prefix: --output_xtc_path
    default: system.xtc

  output_cpt_path:
    label: Path to the output GROMACS checkpoint file CPT
    doc: |-
      Path to the output GROMACS checkpoint file CPT
      Type: string
      File type: output
      Accepted formats: cpt
      Example file: null
    type: string
    format:
    - edam:format_2333
    inputBinding:
      prefix: --output_cpt_path
    default: system.cpt

  output_dhdl_path:
    label: Path to the output dhdl.xvg file only used when free energy calculation
      is turned on
    doc: |-
      Path to the output dhdl.xvg file only used when free energy calculation is turned on
      Type: string
      File type: output
      Accepted formats: xvg
      Example file: null
    type: string
    format:
    - edam:format_2033
    inputBinding:
      prefix: --output_dhdl_path
    default: system.xvg

  config:
    label: Advanced configuration options for biobb_gromacs Mdrun
    doc: |-
      Advanced configuration options for biobb_gromacs Mdrun. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_gromacs Mdrun documentation: https://biobb-gromacs.readthedocs.io/en/latest/gromacs.html#module-gromacs.mdrun
    type: string?
    inputBinding:
      prefix: --config
CWL Gromacs From line 11 of biobb_adapters/mdrun.cwl 
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baseCommand: pdb2gmx

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

inputs:
  input_pdb_path:
    label: Path to the input PDB file
    doc: |-
      Path to the input PDB file
      Type: string
      File type: input
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/egfr.pdb
    type: File
    format:
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_pdb_path

  output_gro_path:
    label: Path to the output GRO file
    doc: |-
      Path to the output GRO file
      Type: string
      File type: output
      Accepted formats: gro
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_pdb2gmx.gro
    type: string
    format:
    - edam:format_2033
    inputBinding:
      position: 2
      prefix: --output_gro_path
    default: system.gro

  output_top_zip_path:
    label: Path the output TOP topology in zip format
    doc: |-
      Path the output TOP topology in zip format
      Type: string
      File type: output
      Accepted formats: zip
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_pdb2gmx.zip
    type: string
    format:
    - edam:format_3987
    inputBinding:
      position: 3
      prefix: --output_top_zip_path
    default: system.zip

  config:
    label: Advanced configuration options for biobb_gromacs Pdb2gmx
    doc: |-
      Advanced configuration options for biobb_gromacs Pdb2gmx. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_gromacs Pdb2gmx documentation: https://biobb-gromacs.readthedocs.io/en/latest/gromacs.html#module-gromacs.pdb2gmx
    type: string?
    inputBinding:
      prefix: --config
CWL From line 11 of biobb_adapters/pdb2gmx.cwl 
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baseCommand: reduce_remove_hydrogens

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
      Example file: https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/data/ambertools/reduce.H.pdb
    type: File
    format:
    - edam:format_1476
    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
      Example file: https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/ambertools/ref_reduce.remove.pdb
    type: string
    format:
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --output_path
    default: system.pdb

  config:
    label: Advanced configuration options for biobb_chemistry ReduceRemoveHydrogens
    doc: |-
      Advanced configuration options for biobb_chemistry ReduceRemoveHydrogens. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_chemistry ReduceRemoveHydrogens documentation: https://biobb-chemistry.readthedocs.io/en/latest/ambertools.html#module-ambertools.reduce_remove_hydrogens
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_chemistry From line 12 of biobb_adapters/reduce_remove_hydrogens.cwl 
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baseCommand: solvate

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

inputs:
  input_solute_gro_path:
    label: Path to the input GRO file
    doc: |-
      Path to the input GRO file
      Type: string
      File type: input
      Accepted formats: gro, pdb
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/solvate.gro
    type: File
    format:
    - edam:format_2033
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_solute_gro_path

  output_gro_path:
    label: Path to the output GRO file
    doc: |-
      Path to the output GRO file
      Type: string
      File type: output
      Accepted formats: gro, pdb
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_solvate.gro
    type: string
    format:
    - edam:format_2033
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --output_gro_path
    default: system.gro

  input_top_zip_path:
    label: Path the input TOP topology in zip format
    doc: |-
      Path the input TOP topology in zip format
      Type: string
      File type: input
      Accepted formats: zip
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/solvate.zip
    type: File
    format:
    - edam:format_3987
    inputBinding:
      position: 3
      prefix: --input_top_zip_path

  output_top_zip_path:
    label: Path the output topology in zip format
    doc: |-
      Path the output topology in zip format
      Type: string
      File type: output
      Accepted formats: zip
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_solvate.zip
    type: string
    format:
    - edam:format_3987
    inputBinding:
      position: 4
      prefix: --output_top_zip_path
    default: system.zip

  input_solvent_gro_path:
    label: (spc216.gro) Path to the GRO file containing the structure of the solvent
    doc: |-
      (spc216.gro) Path to the GRO file containing the structure of the solvent
      Type: string
      File type: input
      Accepted formats: gro
      Example file: null
    type: File?
    format:
    - edam:format_2033
    inputBinding:
      prefix: --input_solvent_gro_path

  config:
    label: Advanced configuration options for biobb_gromacs Solvate
    doc: |-
      Advanced configuration options for biobb_gromacs Solvate. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_gromacs Solvate documentation: https://biobb-gromacs.readthedocs.io/en/latest/gromacs.html#module-gromacs.solvate
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_gromacs From line 11 of biobb_adapters/solvate.cwl
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/bioexcel/biobb_workflows/tree/master/biobb_wf_protein_complex_md_setup/cwl
Name: cwl-protein-ligand-complex-md-setup-tutorial
Version: Version 2
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License: Boost Software License 1.0
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