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.

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SEEK ID: https://workflowhub.eu/workflows/289?version=2

DOI: 10.48546/workflowhub.workflow.289.2

Inputs

ID Name Description Type
mutations_list List of mutations List of mutations to perform the workflow on.
  • array containing
    • string
step0_reduce_remove_hydrogens_input_path Input file Path to the input file.
  • File
step0_reduce_remove_hydrogens_output_path Output file Path to the output file.
  • string
step1_extract_molecule_output_molecule_path Output file Output molecule file path.
  • string
step00_cat_pdb_input_structure2 Input file Input structure 2 file path.
  • File
step00_cat_pdb_output_structure_path Output file Output protein file path.
  • string
step2_fix_side_chain_output_pdb_path Output file Output PDB file path.
  • string
step3_mutate_output_pdb_path Output file Output PDB file path.
  • string
step4_pdb2gmx_config Config file Configuration file for biobb_gromacs.pdb2gmx tool.
  • string
step4_pdb2gmx_output_gro_path Output file Path to the output GRO file.
  • string
step4_pdb2gmx_output_top_zip_path Output file Path the output TOP topology in zip format.
  • string
step5_editconf_config Config file Configuration file for biobb_gromacs.editconf tool.
  • string
step5_editconf_output_gro_path Output file Path to the output GRO file.
  • string
step6_solvate_output_gro_path Output file Path to the output GRO file.
  • string
step6_solvate_output_top_zip_path Output file Path the output topology in zip format.
  • string
step7_grompp_genion_config Config file Configuration file for biobb_gromacs.grompp tool.
  • string
step7_grompp_genion_output_tpr_path Output file Path to the output portable binary run file TPR.
  • string
step8_genion_config Config file Configuration file for biobb_gromacs.grompp tool.
  • string
step8_genion_output_gro_path Output file Path to the input structure GRO file.
  • string
step8_genion_output_top_zip_path Output file Path the output topology TOP and ITP files zipball.
  • string
step9_grompp_min_config Config file Configuration file for biobb_gromacs.grompp tool.
  • string
step9_grompp_min_output_tpr_path Output file Path to the output portable binary run file TPR.
  • string
step10_mdrun_min_output_trr_path Output file Path to the GROMACS uncompressed raw trajectory file TRR.
  • string
step10_mdrun_min_output_gro_path Output file Path to the output GROMACS structure GRO file.
  • string
step10_mdrun_min_output_edr_path Output file Path to the output GROMACS portable energy file EDR.
  • string
step10_mdrun_min_output_log_path Output file Path to the output GROMACS trajectory log file LOG.
  • string
step100_make_ndx_config Config file Configuration file for biobb_gromacs.make_ndx tool.
  • string
step100_make_ndx_output_ndx_path Output file Path to the output index NDX file.
  • string
step11_grompp_nvt_config Config file Configuration file for biobb_gromacs.grompp tool.
  • string
step11_grompp_nvt_output_tpr_path Output file Path to the output portable binary run file TPR.
  • string
step12_mdrun_nvt_output_trr_path Output file Path to the GROMACS uncompressed raw trajectory file TRR.
  • string
step12_mdrun_nvt_output_gro_path Output file Path to the output GROMACS structure GRO file.
  • string
step12_mdrun_nvt_output_edr_path Output file Path to the output GROMACS portable energy file EDR.
  • string
step12_mdrun_nvt_output_log_path Output file Path to the output GROMACS trajectory log file LOG.
  • string
step12_mdrun_nvt_output_cpt_path Output file Path to the output GROMACS checkpoint file CPT.
  • string
step13_grompp_npt_config Config file Configuration file for biobb_gromacs.grompp tool.
  • string
step13_grompp_npt_output_tpr_path Output file Path to the output portable binary run file TPR.
  • string
step14_mdrun_npt_output_trr_path Output file Path to the GROMACS uncompressed raw trajectory file TRR.
  • string
step14_mdrun_npt_output_gro_path Output file Path to the output GROMACS structure GRO file.
  • string
step14_mdrun_npt_output_edr_path Output file Path to the output GROMACS portable energy file EDR.
  • string
step14_mdrun_npt_output_log_path Output file Path to the output GROMACS trajectory log file LOG.
  • string
step14_mdrun_npt_output_cpt_path Output file Path to the output GROMACS checkpoint file CPT.
  • string
step15_grompp_md_config Config file Configuration file for biobb_gromacs.grompp tool.
  • string
step15_grompp_md_output_tpr_path Output file Path to the output portable binary run file TPR.
  • string
step16_mdrun_md_output_trr_path Output file Path to the GROMACS uncompressed raw trajectory file TRR.
  • string
step16_mdrun_md_output_gro_path Output file Path to the output GROMACS structure GRO file.
  • string
step16_mdrun_md_output_edr_path Output file Path to the output GROMACS portable energy file EDR.
  • string
step16_mdrun_md_output_log_path Output file Path to the output GROMACS trajectory log file LOG.
  • string
step16_mdrun_md_output_cpt_path Output file Path to the output GROMACS checkpoint file CPT.
  • string
step17_gmx_image1_config Config file Configuration file for biobb_analysis.gmx_image tool.
  • string
step17_gmx_image1_output_traj_path Output file Path to the output file.
  • string
step18_gmx_image2_config Config file Configuration file for biobb_analysis.gmx_image tool.
  • string
step18_gmx_image2_output_traj_path Output file Path to the output file.
  • string
step19_gmx_trjconv_str_config Config file Configuration file for biobb_analysis.gmx_trjconv_str tool.
  • string
step19_gmx_trjconv_str_output_str_path Output file Path to the output file.
  • string
step20_gmx_energy_config Config file Configuration file for biobb_analysis.gmx_energy tool.
  • string
step20_gmx_energy_output_xvg_path Output file Path to the XVG output file.
  • string
step21_gmx_rgyr_config Config file Configuration file for biobb_analysis.gmx_rgyr tool.
  • string
step21_gmx_rgyr_output_xvg_path Output file Path to the XVG output file.
  • string
step22_rmsd_first_config Config file Configuration file for biobb_analysis.gmx_rms tool.
  • string
step22_rmsd_first_output_xvg_path Output file Path to the XVG output file.
  • string
step23_rmsd_exp_config Config file Configuration file for biobb_analysis.gmx_rms tool.
  • string
step23_rmsd_exp_output_xvg_path Output file Path to the XVG output file.
  • string
step24_grompp_md_config Config file Configuration file for biobb_gromacs.grompp tool.
  • string
step24_grompp_md_output_tpr_path Output file Path to the output portable binary run file TPR.
  • 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 Subworkflow Subworkflow executed for each mutation.

Outputs

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

Version History

Version 2 (latest) 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
Creators
Submitter
Discussion Channel
BioExcel Workflows
Citation
Hospital, A., & Bayarri, G. (2023). CWL Protein MD Setup tutorial with mutations. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.289.2
License
Apache License 2.0
Activity

Views: 1986   Downloads: 536

Created: 17th Mar 2022 at 13:22

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