global_properties:
  working_dir_path: biobb_wf_ligand_parameterization
  can_write_console_log: False


step2_babel_minimize:
  tool: babel_minimize
  paths:
    input_path: /data/ligand.pdb
    output_path: ligand.H.min.mol2
  properties:
    criteria: 1e-10
    method: sd
    force_field: GAFF
    hydrogens: false

step3_acpype_params_gmx:
  tool: acpype_params_gmx
  paths:
    input_path: dependency/step2_babel_minimize/output_path
    output_path_gro: output.params.gro
    output_path_itp: output.params.itp
    output_path_top: output.params.top
  properties:
    basename: biobb_GMX_LP
    charge: -1