CWL Amber Protein MD Setup tutorial

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AMBER Protein MD Setup tutorials 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 , step by step, using the BioExcel Building Blocks library (biobb) wrapping the Ambertools MD package .

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: amber_to_pdb

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

inputs:
  input_top_path:
    label: AMBER topology file
    doc: |-
      AMBER topology file
      Type: string
      File type: input
      Accepted formats: top, parmtop, prmtop
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/ambpdb/structure.leap.top
    type: File
    format:
    - edam:format_3881
    - edam:format_3881
    - edam:format_3881
    inputBinding:
      position: 1
      prefix: --input_top_path

  input_crd_path:
    label: AMBER coordinates file
    doc: |-
      AMBER coordinates file
      Type: string
      File type: input
      Accepted formats: crd, mdcrd, inpcrd, rst
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/ambpdb/structure.leap.crd
    type: File
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3878
    - edam:format_3886
    inputBinding:
      position: 2
      prefix: --input_crd_path

  output_pdb_path:
    label: Structure PDB file
    doc: |-
      Structure PDB file
      Type: string
      File type: output
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/ambpdb/structure.ambpdb.pdb
    type: string
    format:
    - edam:format_1476
    inputBinding:
      position: 3
      prefix: --output_pdb_path
    default: system.pdb

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

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

inputs:
  input_top_path:
    label: Path to the input structure or topology file
    doc: |-
      Path to the input structure or topology file
      Type: string
      File type: input
      Accepted formats: top, pdb, prmtop, parmtop, zip
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top
    type: File
    format:
    - edam:format_3881
    - edam:format_1476
    - edam:format_3881
    - edam:format_3881
    - edam:format_3987
    inputBinding:
      position: 1
      prefix: --input_top_path

  input_traj_path:
    label: Path to the input trajectory to be processed
    doc: |-
      Path to the input trajectory to be processed
      Type: string
      File type: input
      Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd
    type: File
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3650
    - edam:format_3650
    - edam:format_3650
    - edam:format_3886
    - edam:format_3886
    - edam:format_3886
    - edam:format_3878
    - edam:format_3887
    - edam:format_2033
    - edam:format_1476
    - edam:format_3816
    - edam:format_3910
    - edam:format_2033
    - edam:format_3885
    - edam:format_3875
    - edam:format_1477
    - edam:format_2333
    - edam:format_2033
    - edam:format_3814
    - edam:format_2033
    inputBinding:
      position: 2
      prefix: --input_traj_path

  output_cpptraj_path:
    label: Path to the output processed trajectory
    doc: |-
      Path to the output processed trajectory
      Type: string
      File type: output
      Accepted formats: mdcrd, crd, netcdf, nc, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.image.netcdf
    type: string
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3650
    - edam:format_3650
    - edam:format_3886
    - edam:format_2033
    - edam:format_3878
    - edam:format_1476
    - edam:format_3816
    - edam:format_3885
    - edam:format_3910
    - edam:format_3875
    - edam:format_2033
    inputBinding:
      position: 3
      prefix: --output_cpptraj_path
    default: system.mdcrd

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

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

inputs:
  input_top_path:
    label: Path to the input structure or topology file
    doc: |-
      Path to the input structure or topology file
      Type: string
      File type: input
      Accepted formats: top, pdb, prmtop, parmtop, zip
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top
    type: File
    format:
    - edam:format_3881
    - edam:format_1476
    - edam:format_3881
    - edam:format_3881
    - edam:format_3987
    inputBinding:
      position: 1
      prefix: --input_top_path

  input_traj_path:
    label: Path to the input trajectory to be processed
    doc: |-
      Path to the input trajectory to be processed
      Type: string
      File type: input
      Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd
    type: File
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3650
    - edam:format_3650
    - edam:format_3650
    - edam:format_3886
    - edam:format_3886
    - edam:format_3886
    - edam:format_3878
    - edam:format_3887
    - edam:format_2033
    - edam:format_1476
    - edam:format_3816
    - edam:format_3910
    - edam:format_2033
    - edam:format_3885
    - edam:format_3875
    - edam:format_1477
    - edam:format_2333
    - edam:format_2033
    - edam:format_3814
    - edam:format_2033
    inputBinding:
      position: 2
      prefix: --input_traj_path

  output_cpptraj_path:
    label: Path to the output analysis
    doc: |-
      Path to the output analysis
      Type: string
      File type: output
      Accepted formats: dat, agr, xmgr, gnu
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.rgyr.dat
    type: string
    format:
    - edam:format_1637
    - edam:format_2033
    - edam:format_2033
    - edam:format_2033
    inputBinding:
      position: 3
      prefix: --output_cpptraj_path
    default: system.dat

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

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

inputs:
  input_top_path:
    label: Path to the input structure or topology file
    doc: |-
      Path to the input structure or topology file
      Type: string
      File type: input
      Accepted formats: top, pdb, prmtop, parmtop, zip
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top
    type: File
    format:
    - edam:format_3881
    - edam:format_1476
    - edam:format_3881
    - edam:format_3881
    - edam:format_3987
    inputBinding:
      position: 1
      prefix: --input_top_path

  input_traj_path:
    label: Path to the input trajectory to be processed
    doc: |-
      Path to the input trajectory to be processed
      Type: string
      File type: input
      Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd
    type: File
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3650
    - edam:format_3650
    - edam:format_3650
    - edam:format_3886
    - edam:format_3886
    - edam:format_3886
    - edam:format_3878
    - edam:format_3887
    - edam:format_2033
    - edam:format_1476
    - edam:format_3816
    - edam:format_3910
    - edam:format_2033
    - edam:format_3885
    - edam:format_3875
    - edam:format_1477
    - edam:format_2333
    - edam:format_2033
    - edam:format_3814
    - edam:format_2033
    inputBinding:
      position: 2
      prefix: --input_traj_path

  output_cpptraj_path:
    label: Path to the output processed analysis
    doc: |-
      Path to the output processed analysis
      Type: string
      File type: output
      Accepted formats: dat, agr, xmgr, gnu
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.rms.first.dat
    type: string
    format:
    - edam:format_1637
    - edam:format_2033
    - edam:format_2033
    - edam:format_2033
    inputBinding:
      position: 3
      prefix: --output_cpptraj_path
    default: system.dat

  input_exp_path:
    label: Path to the experimental reference file (required if reference = experimental)
    doc: |-
      Path to the experimental reference file (required if reference = experimental)
      Type: string
      File type: input
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/experimental.1e5t.pdb
    type: File?
    format:
    - edam:format_1476
    inputBinding:
      prefix: --input_exp_path

  output_traj_path:
    label: Path to the output processed trajectory
    doc: |-
      Path to the output processed trajectory
      Type: string
      File type: output
      Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd
    type: string
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3650
    - edam:format_3650
    - edam:format_3650
    - edam:format_3886
    - edam:format_3886
    - edam:format_3886
    - edam:format_3878
    - edam:format_3887
    - edam:format_2033
    - edam:format_1476
    - edam:format_3816
    - edam:format_3910
    - edam:format_2033
    - edam:format_3885
    - edam:format_3875
    - edam:format_1477
    - edam:format_2333
    - edam:format_2033
    - edam:format_3814
    - edam:format_2033
    inputBinding:
      prefix: --output_traj_path
    default: system.mdcrd

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

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

inputs:
  input_pdb_path:
    label: Input 3D structure PDB file
    doc: |-
      Input 3D structure PDB file
      Type: string
      File type: input
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/structure.solv.pdb
    type: File
    format:
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_pdb_path

  output_pdb_path:
    label: Output 3D structure PDB file matching the topology file
    doc: |-
      Output 3D structure PDB file matching the topology file
      Type: string
      File type: output
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.ions.pdb
    type: string
    format:
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --output_pdb_path
    default: system.pdb

  output_top_path:
    label: Output topology file (AMBER ParmTop)
    doc: |-
      Output topology file (AMBER ParmTop)
      Type: string
      File type: output
      Accepted formats: top, parmtop, prmtop
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.ions.top
    type: string
    format:
    - edam:format_3881
    - edam:format_3881
    - edam:format_3881
    inputBinding:
      position: 3
      prefix: --output_top_path
    default: system.top

  output_crd_path:
    label: Output coordinates file (AMBER crd)
    doc: |-
      Output coordinates file (AMBER crd)
      Type: string
      File type: output
      Accepted formats: crd, mdcrd, inpcrd
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.ions.crd
    type: string
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3878
    inputBinding:
      position: 4
      prefix: --output_crd_path
    default: system.crd

  input_lib_path:
    label: Input ligand library parameters file
    doc: |-
      Input ligand library parameters file
      Type: string
      File type: input
      Accepted formats: lib, zip
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/ligand.lib
    type: File?
    format:
    - edam:format_3889
    - edam:format_3987
    inputBinding:
      prefix: --input_lib_path

  input_frcmod_path:
    label: Input ligand frcmod parameters file
    doc: |-
      Input ligand frcmod parameters file
      Type: string
      File type: input
      Accepted formats: frcmod, zip
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/ligand.frcmod
    type: File?
    format:
    - edam:format_3888
    - edam:format_3987
    inputBinding:
      prefix: --input_frcmod_path

  input_params_path:
    label: Additional leap parameter files to load with loadAmberParams Leap command
    doc: |-
      Additional leap parameter files to load with loadAmberParams Leap command
      Type: string
      File type: input
      Accepted formats: in, leapin, txt, zip
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/frcmod.ionsdang_spce.txt
    type: File?
    format:
    - edam:format_2330
    - edam:format_2330
    - edam:format_2330
    - edam:format_3987
    inputBinding:
      prefix: --input_params_path

  input_source_path:
    label: Additional leap command files to load with source Leap command
    doc: |-
      Additional leap command files to load with source Leap command
      Type: string
      File type: input
      Accepted formats: in, leapin, txt, zip
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/leaprc.water.spce.txt
    type: File?
    format:
    - edam:format_2330
    - edam:format_2330
    - edam:format_2330
    - edam:format_3987
    inputBinding:
      prefix: --input_source_path

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

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

inputs:
  input_pdb_path:
    label: Input 3D structure PDB file
    doc: |-
      Input 3D structure PDB file
      Type: string
      File type: input
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/structure.leapin.pdb
    type: File
    format:
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_pdb_path

  output_pdb_path:
    label: Output 3D structure PDB file matching the topology file
    doc: |-
      Output 3D structure PDB file matching the topology file
      Type: string
      File type: output
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.leap.pdb
    type: string
    format:
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --output_pdb_path
    default: system.pdb

  output_top_path:
    label: Output topology file (AMBER ParmTop)
    doc: |-
      Output topology file (AMBER ParmTop)
      Type: string
      File type: output
      Accepted formats: top, parmtop, prmtop
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.leap.top
    type: string
    format:
    - edam:format_3881
    - edam:format_3881
    - edam:format_3881
    inputBinding:
      position: 3
      prefix: --output_top_path
    default: system.top

  output_crd_path:
    label: Output coordinates file (AMBER crd)
    doc: |-
      Output coordinates file (AMBER crd)
      Type: string
      File type: output
      Accepted formats: crd, mdcrd, inpcrd
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.leap.crd
    type: string
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3878
    inputBinding:
      position: 4
      prefix: --output_crd_path
    default: system.crd

  input_lib_path:
    label: Input ligand library parameters file
    doc: |-
      Input ligand library parameters file
      Type: string
      File type: input
      Accepted formats: lib, zip
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/ligand.lib
    type: File?
    format:
    - edam:format_3889
    - edam:format_3987
    inputBinding:
      prefix: --input_lib_path

  input_frcmod_path:
    label: Input ligand frcmod parameters file
    doc: |-
      Input ligand frcmod parameters file
      Type: string
      File type: input
      Accepted formats: frcmod, zip
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/ligand.frcmod
    type: File?
    format:
    - edam:format_3888
    - edam:format_3987
    inputBinding:
      prefix: --input_frcmod_path

  input_params_path:
    label: Additional leap parameter files to load with loadAmberParams Leap command
    doc: |-
      Additional leap parameter files to load with loadAmberParams Leap command
      Type: string
      File type: input
      Accepted formats: in, leapin, txt, zip
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/frcmod.ionsdang_spce.txt
    type: File?
    format:
    - edam:format_2330
    - edam:format_2330
    - edam:format_2330
    - edam:format_3987
    inputBinding:
      prefix: --input_params_path

  input_source_path:
    label: Additional leap command files to load with source Leap command
    doc: |-
      Additional leap command files to load with source Leap command
      Type: string
      File type: input
      Accepted formats: in, leapin, txt, zip
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/leaprc.water.spce.txt
    type: File?
    format:
    - edam:format_2330
    - edam:format_2330
    - edam:format_2330
    - edam:format_3987
    inputBinding:
      prefix: --input_source_path

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

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

inputs:
  input_pdb_path:
    label: Input 3D structure PDB file
    doc: |-
      Input 3D structure PDB file
      Type: string
      File type: input
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/structure.leap.pdb
    type: File
    format:
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_pdb_path

  output_pdb_path:
    label: Output 3D structure PDB file matching the topology file
    doc: |-
      Output 3D structure PDB file matching the topology file
      Type: string
      File type: output
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.solv.pdb
    type: string
    format:
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --output_pdb_path
    default: system.pdb

  output_top_path:
    label: Output topology file (AMBER ParmTop)
    doc: |-
      Output topology file (AMBER ParmTop)
      Type: string
      File type: output
      Accepted formats: top, parmtop, prmtop
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.solv.top
    type: string
    format:
    - edam:format_3881
    - edam:format_3881
    - edam:format_3881
    inputBinding:
      position: 3
      prefix: --output_top_path
    default: system.top

  output_crd_path:
    label: Output coordinates file (AMBER crd)
    doc: |-
      Output coordinates file (AMBER crd)
      Type: string
      File type: output
      Accepted formats: crd, mdcrd, inpcrd
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.solv.crd
    type: string
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3878
    inputBinding:
      position: 4
      prefix: --output_crd_path
    default: system.crd

  input_lib_path:
    label: Input ligand library parameters file
    doc: |-
      Input ligand library parameters file
      Type: string
      File type: input
      Accepted formats: lib, zip
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/ligand.lib
    type: File?
    format:
    - edam:format_3889
    - edam:format_3987
    inputBinding:
      prefix: --input_lib_path

  input_frcmod_path:
    label: Input ligand frcmod parameters file
    doc: |-
      Input ligand frcmod parameters file
      Type: string
      File type: input
      Accepted formats: frcmod, zip
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/ligand.frcmod
    type: File?
    format:
    - edam:format_3888
    - edam:format_3987
    inputBinding:
      prefix: --input_frcmod_path

  input_params_path:
    label: Additional leap parameter files to load with loadAmberParams Leap command
    doc: |-
      Additional leap parameter files to load with loadAmberParams Leap command
      Type: string
      File type: input
      Accepted formats: in, leapin, txt, zip
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/frcmod.ionsdang_spce.txt
    type: File?
    format:
    - edam:format_2330
    - edam:format_2330
    - edam:format_2330
    - edam:format_3987
    inputBinding:
      prefix: --input_params_path

  input_source_path:
    label: Additional leap command files to load with source Leap command
    doc: |-
      Additional leap command files to load with source Leap command
      Type: string
      File type: input
      Accepted formats: in, leapin, txt, zip
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/leaprc.water.spce.txt
    type: File?
    format:
    - edam:format_2330
    - edam:format_2330
    - edam:format_2330
    - edam:format_3987
    inputBinding:
      prefix: --input_source_path

  config:
    label: Advanced configuration options for biobb_amber LeapSolvate
    doc: |-
      Advanced configuration options for biobb_amber LeapSolvate. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_amber LeapSolvate documentation: https://biobb-amber.readthedocs.io/en/latest/leap.html#module-leap.leap_solvate
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_amber From line 11 of biobb_adapters/leap_solvate.cwl 
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baseCommand: pdb4amber_run

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

inputs:
  input_pdb_path:
    label: Input 3D structure PDB file
    doc: |-
      Input 3D structure PDB file
      Type: string
      File type: input
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/pdb4amber/1aki_fixed.pdb
    type: File
    format:
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_pdb_path

  output_pdb_path:
    label: Output 3D structure PDB file
    doc: |-
      Output 3D structure PDB file
      Type: string
      File type: output
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/pdb4amber/structure.pdb4amber.pdb
    type: string
    format:
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --output_pdb_path
    default: system.pdb

  config:
    label: Advanced configuration options for biobb_amber.pdb4amber.pdb4amber_run
      Pdb4amberRun
    doc: |-
      Advanced configuration options for biobb_amber.pdb4amber.pdb4amber_run Pdb4amberRun. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_amber.pdb4amber.pdb4amber_run Pdb4amberRun documentation: https://biobb-amber.readthedocs.io/en/latest/pdb4amber.html#module-pdb4amber.pdb4amber_run
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_amber From line 11 of biobb_adapters/pdb4amber_run.cwl 
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baseCommand: process_mdout

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

inputs:
  input_log_path:
    label: AMBER (sander) MD output (log) file
    doc: |-
      AMBER (sander) MD output (log) file
      Type: string
      File type: input
      Accepted formats: log, out, txt, o
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/process/sander.heat.log
    type: File
    format:
    - edam:format_2330
    - edam:format_2330
    - edam:format_2330
    - edam:format_2330
    inputBinding:
      position: 1
      prefix: --input_log_path

  output_dat_path:
    label: Dat output file containing data from the specified terms along the minimization
      process
    doc: |-
      Dat output file containing data from the specified terms along the minimization process
      Type: string
      File type: output
      Accepted formats: dat, txt, csv
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/process/sander.md.temp.dat
    type: string
    format:
    - edam:format_1637
    - edam:format_2330
    - edam:format_3752
    inputBinding:
      position: 2
      prefix: --output_dat_path
    default: system.dat

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

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

inputs:
  input_log_path:
    label: AMBER (sander) Minimization output (log) file
    doc: |-
      AMBER (sander) Minimization output (log) file
      Type: string
      File type: input
      Accepted formats: log, out, txt, o
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/process/sander.min.log
    type: File
    format:
    - edam:format_2330
    - edam:format_2330
    - edam:format_2330
    - edam:format_2330
    inputBinding:
      position: 1
      prefix: --input_log_path

  output_dat_path:
    label: Dat output file containing data from the specified terms along the minimization
      process
    doc: |-
      Dat output file containing data from the specified terms along the minimization process
      Type: string
      File type: output
      Accepted formats: dat, txt, csv
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/process/sander.min.energy.dat
    type: string
    format:
    - edam:format_1637
    - edam:format_2330
    - edam:format_3752
    inputBinding:
      position: 2
      prefix: --output_dat_path
    default: system.dat

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

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

inputs:
  input_top_path:
    label: Input topology file (AMBER ParmTop)
    doc: |-
      Input topology file (AMBER ParmTop)
      Type: string
      File type: input
      Accepted formats: top, parmtop, prmtop
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/sander/cln025.prmtop
    type: File
    format:
    - edam:format_3881
    - edam:format_3881
    - edam:format_3881
    inputBinding:
      position: 1
      prefix: --input_top_path

  input_crd_path:
    label: Input coordinates file (AMBER crd)
    doc: |-
      Input coordinates file (AMBER crd)
      Type: string
      File type: input
      Accepted formats: crd, mdcrd, inpcrd, netcdf, nc, ncrst
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/sander/cln025.inpcrd
    type: File
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3878
    - edam:format_3650
    - edam:format_3650
    - edam:format_3886
    inputBinding:
      position: 2
      prefix: --input_crd_path

  output_log_path:
    label: Output log file
    doc: |-
      Output log file
      Type: string
      File type: output
      Accepted formats: log, out, txt, o
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/sander/sander.log
    type: string
    format:
    - edam:format_2330
    - edam:format_2330
    - edam:format_2330
    - edam:format_2330
    inputBinding:
      position: 3
      prefix: --output_log_path
    default: system.log

  output_traj_path:
    label: Output trajectory file
    doc: |-
      Output trajectory file
      Type: string
      File type: output
      Accepted formats: trj, crd, mdcrd, x, netcdf, nc
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/sander/sander.x
    type: string
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3878
    - edam:format_3878
    - edam:format_3650
    - edam:format_3650
    inputBinding:
      position: 4
      prefix: --output_traj_path
    default: system.trj

  output_rst_path:
    label: Output restart file
    doc: |-
      Output restart file
      Type: string
      File type: output
      Accepted formats: rst, rst7, netcdf, nc, ncrst
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/sander/sander.rst
    type: string
    format:
    - edam:format_3886
    - edam:format_3886
    - edam:format_3650
    - edam:format_3650
    - edam:format_3886
    inputBinding:
      position: 5
      prefix: --output_rst_path
    default: system.rst

  input_mdin_path:
    label: Input configuration file (MD run options) (AMBER mdin)
    doc: |-
      Input configuration file (MD run options) (AMBER mdin)
      Type: string
      File type: input
      Accepted formats: mdin, in, txt
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/sander/npt.mdin
    type: File?
    format:
    - edam:format_2330
    - edam:format_2330
    - edam:format_2330
    inputBinding:
      prefix: --input_mdin_path

  input_cpin_path:
    label: Input constant pH file (AMBER cpin)
    doc: |-
      Input constant pH file (AMBER cpin)
      Type: string
      File type: input
      Accepted formats: cpin
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/sander/cln025.cpin
    type: File?
    format:
    - edam:format_2330
    inputBinding:
      prefix: --input_cpin_path

  input_ref_path:
    label: Input reference coordinates for position restraints
    doc: |-
      Input reference coordinates for position restraints
      Type: string
      File type: input
      Accepted formats: rst, rst7, netcdf, nc, ncrst, crd
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/sander/sander.rst
    type: File?
    format:
    - edam:format_3886
    - edam:format_3886
    - edam:format_3650
    - edam:format_3650
    - edam:format_3886
    - edam:format_3878
    inputBinding:
      prefix: --input_ref_path

  output_cpout_path:
    label: Output constant pH file (AMBER cpout)
    doc: |-
      Output constant pH file (AMBER cpout)
      Type: string
      File type: output
      Accepted formats: cpout
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/sander/sander.cpout
    type: string
    format:
    - edam:format_2330
    inputBinding:
      prefix: --output_cpout_path
    default: system.cpout

  output_cprst_path:
    label: Output constant pH restart file (AMBER rstout)
    doc: |-
      Output constant pH restart file (AMBER rstout)
      Type: string
      File type: output
      Accepted formats: cprst, rst, rst7
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/sander/sander.cprst
    type: string
    format:
    - edam:format_3886
    - edam:format_3886
    - edam:format_3886
    inputBinding:
      prefix: --output_cprst_path
    default: system.cprst

  output_mdinfo_path:
    label: Output MD info
    doc: |-
      Output MD info
      Type: string
      File type: output
      Accepted formats: mdinfo
      Example file: https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/sander/sander.mdinfo
    type: string
    format:
    - edam:format_2330
    inputBinding:
      prefix: --output_mdinfo_path
    default: system.mdinfo

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