Workflow Type: Common Workflow Language
Stable

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.

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
Discussion Channel
Citation
Hospital, A., & Bayarri, G. (2023). CWL Protein MD Setup tutorial with mutations. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.289.2
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Views: 1105

Created: 17th Mar 2022 at 13:22

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