Automatic Ligand parameterization for GROMACS
Version 1

Workflow Type: Common Workflow Language

This workflow performs the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb). The parameters generated are topologies for GROMACS.


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


ID Name Description
step2_babel_minimize BabelMinimize Energetically minimize small molecules.
step3_acpype_params_gmx AcpypeParamsGMX Small molecule parameterization for GROMACS MD package.


ID Name Description Type
step2_babel_minimize_out1 output_path Path to the output file
  • File
step3_acpype_params_gmx_out1 output_path_gro Path to the GRO output file
  • File
step3_acpype_params_gmx_out2 output_path_itp Path to the ITP output file
  • File
step3_acpype_params_gmx_out3 output_path_top Path to the TOP output file
  • File
Total size: 2.31 KB
help Creators and Submitter
Bayarri, G., & Hospital, A. (2022). Automatic Ligand parameterization for GROMACS. WorkflowHub.

Views: 90   Downloads: 0

Created: 10th Jan 2022 at 10:39

Last used: 26th Jan 2022 at 14:56

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Version History

Version 1 (earliest) Created 10th Jan 2022 at 10:39 by Genís Bayarri

Added/updated 1 files

Open master f08983f

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