CWL Protein MD Setup tutorial
Version 1

Workflow Type: Common Workflow Language
Stable

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.

Inputs

ID Name Description Type
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
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.
step4_pdb2gmx Pdb2gmx Creates a compressed (ZIP) GROMACS topology (TOP and ITP files) from a given PDB file.
step5_editconf Editconf Creates a GROMACS structure file (GRO) adding the information of the solvent box to the input structure file.
step6_solvate Solvate Creates a new compressed GROMACS topology file adding solvent molecules to a given input compressed GROMACS topology file.
step7_grompp_genion Grompp Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology.
step8_genion Genion Creates a new compressed GROMACS topology adding ions until reaching the desired concentration to the input compressed GROMACS topology.
step9_grompp_min Grompp Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology.
step10_mdrun_min Mdrun Performs molecular dynamics simulations from an input GROMACS TPR file.
step100_make_ndx MakeNdx Creates a GROMACS index file (NDX) from an input selection and an input GROMACS structure file.
step11_grompp_nvt Grompp Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology.
step12_mdrun_nvt Mdrun Performs molecular dynamics simulations from an input GROMACS TPR file.
step13_grompp_npt Grompp Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology.
step14_mdrun_npt Mdrun Performs molecular dynamics simulations from an input GROMACS TPR file.
step15_grompp_md Grompp Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology.
step16_mdrun_md Mdrun Performs molecular dynamics simulations from an input GROMACS TPR file.
step17_gmx_image1 GMXImage Wrapper of the GROMACS trjconv module for correcting periodicity (image) from a given GROMACS compatible trajectory file.
step18_gmx_image2 GMXImage Wrapper of the GROMACS trjconv module for correcting periodicity (image) from a given GROMACS compatible trajectory file.
step19_gmx_trjconv_str GMXTrjconvStr Wrapper of the GROMACS trjconv module for converting between GROMACS compatible structure file formats and/or extracting a selection of atoms.
step20_gmx_energy GMXEnergy Wrapper of the GROMACS energy module for extracting energy components from a given GROMACS energy file.
step21_gmx_rgyr GMXRgyr Wrapper of the GROMACS gyrate module for computing the radius of gyration (Rgyr) of a molecule about the x-, y- and z-axes, as a function of time, from a given GROMACS compatible trajectory.
step22_rmsd_first GMXRms Wrapper of the GROMACS module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.
step23_rmsd_exp GMXRms Wrapper of the GROMACS module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.
step24_grompp_md Grompp Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology.

Outputs

ID Name Description Type
step0_reduce_remove_hydrogens_out1 output_path Path to the output file
  • File
step1_extract_molecule_out1 output_molecule_path Output molecule file path
  • File
step00_cat_pdb_out1 output_structure_path Output protein file path
  • File
step2_fix_side_chain_out1 output_pdb_path Output PDB file path
  • File
step4_pdb2gmx_out1 output_gro_path Path to the output GRO file
  • File
step4_pdb2gmx_out2 output_top_zip_path Path the output TOP topology in zip format
  • File
step5_editconf_out1 output_gro_path Path to the output GRO file
  • File
step6_solvate_out1 output_gro_path Path to the output GRO file
  • File
step6_solvate_out2 output_top_zip_path Path the output topology in zip format
  • File
step7_grompp_genion_out1 output_tpr_path Path to the output portable binary run file TPR
  • File
step8_genion_out1 output_gro_path Path to the input structure GRO file
  • File
step8_genion_out2 output_top_zip_path Path the output topology TOP and ITP files zipball
  • File
step9_grompp_min_out1 output_tpr_path Path to the output portable binary run file TPR
  • File
step10_mdrun_min_out1 output_trr_path Path to the GROMACS uncompressed raw trajectory file TRR
  • File
step10_mdrun_min_out2 output_gro_path Path to the output GROMACS structure GRO file
  • File
step10_mdrun_min_out3 output_edr_path Path to the output GROMACS portable energy file EDR
  • File
step10_mdrun_min_out4 output_log_path Path to the output GROMACS trajectory log file LOG
  • File
step100_make_ndx_out1 output_ndx_path Path to the output index NDX file
  • File
step11_grompp_nvt_out1 output_tpr_path Path to the output portable binary run file TPR
  • File
step12_mdrun_nvt_out1 output_trr_path Path to the GROMACS uncompressed raw trajectory file TRR
  • File
step12_mdrun_nvt_out2 output_gro_path Path to the output GROMACS structure GRO file
  • File
step12_mdrun_nvt_out3 output_edr_path Path to the output GROMACS portable energy file EDR
  • File
step12_mdrun_nvt_out4 output_log_path Path to the output GROMACS trajectory log file LOG
  • File
step12_mdrun_nvt_out5 output_cpt_path Path to the output GROMACS checkpoint file CPT
  • File
step13_grompp_npt_out1 output_tpr_path Path to the output portable binary run file TPR
  • File
step14_mdrun_npt_out1 output_trr_path Path to the GROMACS uncompressed raw trajectory file TRR
  • File
step14_mdrun_npt_out2 output_gro_path Path to the output GROMACS structure GRO file
  • File
step14_mdrun_npt_out3 output_edr_path Path to the output GROMACS portable energy file EDR
  • File
step14_mdrun_npt_out4 output_log_path Path to the output GROMACS trajectory log file LOG
  • File
step14_mdrun_npt_out5 output_cpt_path Path to the output GROMACS checkpoint file CPT
  • File
step15_grompp_md_out1 output_tpr_path Path to the output portable binary run file TPR
  • File
step16_mdrun_md_out1 output_trr_path Path to the GROMACS uncompressed raw trajectory file TRR
  • File
step16_mdrun_md_out2 output_gro_path Path to the output GROMACS structure GRO file
  • File
step16_mdrun_md_out3 output_edr_path Path to the output GROMACS portable energy file EDR
  • File
step16_mdrun_md_out4 output_log_path Path to the output GROMACS trajectory log file LOG
  • File
step16_mdrun_md_out5 output_cpt_path Path to the output GROMACS checkpoint file CPT
  • File
step17_gmx_image1_out1 output_traj_path Path to the output file
  • File
step18_gmx_image2_out1 output_traj_path Path to the output file
  • File
step19_gmx_trjconv_str_out1 output_str_path Path to the output file
  • File
step20_gmx_energy_out1 output_xvg_path Path to the XVG output file
  • File
step21_gmx_rgyr_out1 output_xvg_path Path to the XVG output file
  • File
step22_rmsd_first_out1 output_xvg_path Path to the XVG output file
  • File
step23_rmsd_exp_out1 output_xvg_path Path to the XVG output file
  • File
step24_grompp_md_out1 output_tpr_path Path to the output portable binary run file TPR
  • File

Version History

Version 1 (earliest) Created 17th Mar 2022 at 09:18 by Genís Bayarri

Initial commit


Frozen Version-1 d3361b3
help Creators and Submitter
Citation
Bayarri, G., & Hospital, A. (2022). CWL Protein MD Setup tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.279.1
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Created: 17th Mar 2022 at 09:18

Last used: 28th Nov 2022 at 05:40

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