CWL Protein MD Setup tutorial with mutations

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Mutations Protein 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, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).

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.

Click and drag the diagram to pan, double click or use the controls to zoom.

SEEK ID: https://workflowhub.eu/workflows/289?version=1

DOI: 10.48546/workflowhub.workflow.289.1

Inputs

ID Name Description Type
mutations_list n/a n/a
  • array containing
    • string
step0_reduce_remove_hydrogens_input_path n/a n/a
  • File
step0_reduce_remove_hydrogens_output_path n/a n/a
  • string
step1_extract_molecule_output_molecule_path n/a n/a
  • string
step00_cat_pdb_input_structure2 n/a n/a
  • File
step00_cat_pdb_output_structure_path n/a n/a
  • string
step2_fix_side_chain_output_pdb_path n/a n/a
  • string
step3_mutate_output_pdb_path n/a n/a
  • string
step4_pdb2gmx_config n/a n/a
  • string
step4_pdb2gmx_output_gro_path n/a n/a
  • string
step4_pdb2gmx_output_top_zip_path n/a n/a
  • string
step5_editconf_config n/a n/a
  • string
step5_editconf_output_gro_path n/a n/a
  • string
step6_solvate_output_gro_path n/a n/a
  • string
step6_solvate_output_top_zip_path n/a n/a
  • string
step7_grompp_genion_config n/a n/a
  • string
step7_grompp_genion_output_tpr_path n/a n/a
  • string
step8_genion_config n/a n/a
  • string
step8_genion_output_gro_path n/a n/a
  • string
step8_genion_output_top_zip_path n/a n/a
  • string
step9_grompp_min_config n/a n/a
  • string
step9_grompp_min_output_tpr_path n/a n/a
  • string
step10_mdrun_min_output_trr_path n/a n/a
  • string
step10_mdrun_min_output_gro_path n/a n/a
  • string
step10_mdrun_min_output_edr_path n/a n/a
  • string
step10_mdrun_min_output_log_path n/a n/a
  • string
step100_make_ndx_config n/a n/a
  • string
step100_make_ndx_output_ndx_path n/a n/a
  • string
step11_grompp_nvt_config n/a n/a
  • string
step11_grompp_nvt_output_tpr_path n/a n/a
  • string
step12_mdrun_nvt_output_trr_path n/a n/a
  • string
step12_mdrun_nvt_output_gro_path n/a n/a
  • string
step12_mdrun_nvt_output_edr_path n/a n/a
  • string
step12_mdrun_nvt_output_log_path n/a n/a
  • string
step12_mdrun_nvt_output_cpt_path n/a n/a
  • string
step13_grompp_npt_config n/a n/a
  • string
step13_grompp_npt_output_tpr_path n/a n/a
  • string
step14_mdrun_npt_output_trr_path n/a n/a
  • string
step14_mdrun_npt_output_gro_path n/a n/a
  • string
step14_mdrun_npt_output_edr_path n/a n/a
  • string
step14_mdrun_npt_output_log_path n/a n/a
  • string
step14_mdrun_npt_output_cpt_path n/a n/a
  • string
step15_grompp_md_config n/a n/a
  • string
step15_grompp_md_output_tpr_path n/a n/a
  • string
step16_mdrun_md_output_trr_path n/a n/a
  • string
step16_mdrun_md_output_gro_path n/a n/a
  • string
step16_mdrun_md_output_edr_path n/a n/a
  • string
step16_mdrun_md_output_log_path n/a n/a
  • string
step16_mdrun_md_output_cpt_path n/a n/a
  • string
step17_gmx_image1_config n/a n/a
  • string
step17_gmx_image1_output_traj_path n/a n/a
  • string
step18_gmx_image2_config n/a n/a
  • string
step18_gmx_image2_output_traj_path n/a n/a
  • string
step19_gmx_trjconv_str_config n/a n/a
  • string
step19_gmx_trjconv_str_output_str_path n/a n/a
  • string
step20_gmx_energy_config n/a n/a
  • string
step20_gmx_energy_output_xvg_path n/a n/a
  • string
step21_gmx_rgyr_config n/a n/a
  • string
step21_gmx_rgyr_output_xvg_path n/a n/a
  • string
step22_rmsd_first_config n/a n/a
  • string
step22_rmsd_first_output_xvg_path n/a n/a
  • string
step23_rmsd_exp_config n/a n/a
  • string
step23_rmsd_exp_output_xvg_path n/a n/a
  • string
step24_grompp_md_config n/a n/a
  • string
step24_grompp_md_output_tpr_path n/a n/a
  • string

Steps

ID Name Description
step0_reduce_remove_hydrogens ReduceRemoveHydrogens Removes hydrogen atoms to small molecules.
step1_extract_molecule ExtractMolecule This class is a wrapper of the Structure Checking tool to extract a molecule from a 3D structure.
step00_cat_pdb CatPDB Class to concat two PDB structures in a single PDB file.
step2_fix_side_chain FixSideChain Reconstructs the missing side chains and heavy atoms of the given PDB file.
subworkflow_mutate n/a n/a

Outputs

ID Name Description Type
top_dir Collected Simulation Data Assorted data files output by the workflow
  • array containing
    • Directory

Version History

Version 3 (latest) Created 26th Mar 2026 at 14:39 by Genís Bayarri

Update to BioBB 5.2.*


Frozen Version-3 d49edb5

Version 2 Created 7th Jun 2023 at 13:22 by Genís Bayarri

Updated workflow descriptors


Frozen Version-2 ecea2aa

Version 1 (earliest) Created 17th Mar 2022 at 13:22 by Genís Bayarri

Initial commit


Frozen Version-1 70fda2a
help Creators and Submitter
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Citation
Bayarri, G., & Hospital, A. (2022). CWL Protein MD Setup tutorial with mutations. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.289.1
License
Apache License 2.0 (Apache-2.0)
Activity

Views: 66051   Downloads: 1408

Created: 17th Mar 2022 at 13:22

Last updated: 26th Mar 2026 at 14:40

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