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Protein Ligand Complex 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 in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the T4 lysozyme L99A/M102Q protein (PDB code 3HTB), in complex with the 2-propylphenol small molecule (3-letter Code JZ4).


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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Inputs

ID Name Description Type
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
step2_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
step4_fix_side_chain_output_pdb_path Output file Output PDB file path.
  • string
step5_pdb2gmx_output_gro_path Output file Path to the output GRO file.
  • string
step5_pdb2gmx_output_top_zip_path Output file Path the output TOP topology in zip format.
  • string
step5_pdb2gmx_config Config file Configuration file for biobb_gromacs.pdb2gmx tool.
  • string
step9_make_ndx_input_structure_path Input file Path to the input GRO/PDB/TPR file.
  • File
step9_make_ndx_output_ndx_path Output file Path to the output index NDX file.
  • string
step9_make_ndx_config Config file Configuration file for biobb_gromacs.make_ndx tool.
  • string
step10_genrestr_input_structure_path Input file Path to the input structure PDB, GRO or TPR format.
  • File
step10_genrestr_output_itp_path Output file Path the output ITP topology file with restrains.
  • string
step10_genrestr_config Config file Configuration file for biobb_gromacs.genrestr tool.
  • string
step11_gmx_trjconv_str_protein_output_str_path Output file Path to the output file.
  • string
step11_gmx_trjconv_str_protein_config Config file Configuration file for biobb_analysis.gmx_trjconv_str tool.
  • string
step12_gmx_trjconv_str_ligand_input_structure_path Input file Path to the input structure file.
  • File
step12_gmx_trjconv_str_ligand_input_top_path Input file Path to the GROMACS input topology file.
  • File
step12_gmx_trjconv_str_ligand_output_str_path Output file Path to the output file.
  • string
step12_gmx_trjconv_str_ligand_config Config file Configuration file for biobb_analysis.gmx_trjconv_str tool.
  • string
step13_cat_pdb_hydrogens_output_structure_path Output file Output protein file path.
  • string
step14_append_ligand_input_itp_path Input file Path to the ligand ITP file to be inserted in the topology.
  • File
step14_append_ligand_output_top_zip_path Output file Path/Name the output topology TOP and ITP files zipball.
  • string
step14_append_ligand_config Config file Configuration file for biobb_gromacs.append_ligand tool.
  • string
step15_editconf_output_gro_path Output file Path to the output GRO file.
  • string
step15_editconf_config Config file Configuration file for biobb_gromacs.editconf tool.
  • string
step16_solvate_output_gro_path Output file Path to the output GRO file.
  • string
step16_solvate_output_top_zip_path Output file Path the output topology in zip format.
  • string
step17_grompp_genion_output_tpr_path Output file Path to the output portable binary run file TPR.
  • string
step17_grompp_genion_config Config file Configuration file for biobb_gromacs.grompp tool.
  • string
step18_genion_output_gro_path Output file Path to the input structure GRO file.
  • string
step18_genion_output_top_zip_path Output file Path the output topology TOP and ITP files zipball.
  • string
step18_genion_config Config file Configuration file for biobb_gromacs.genion tool.
  • string
step19_grompp_min_output_tpr_path Output file Path to the output portable binary run file TPR.
  • string
step19_grompp_min_config Config file Configuration file for biobb_gromacs.grompp tool.
  • string
step20_mdrun_min_output_trr_path Output file Path to the GROMACS uncompressed raw trajectory file TRR.
  • string
step20_mdrun_min_output_gro_path Output file Path to the output GROMACS structure GRO file.
  • string
step20_mdrun_min_output_edr_path Output file Path to the output GROMACS portable energy file EDR.
  • string
step20_mdrun_min_output_log_path Output file Path to the output GROMACS trajectory log file LOG.
  • string
step21_gmx_energy_min_output_xvg_path Output file Path to the XVG output file.
  • string
step21_gmx_energy_min_config Config file Configuration file for biobb_analysis.gmx_energy tool.
  • string
step22_make_ndx_output_ndx_path Output file Path to the output index NDX file.
  • string
step22_make_ndx_config Config file Configuration file for biobb_gromacs.make_ndx tool.
  • string
step23_grompp_nvt_output_tpr_path Output file Path to the output portable binary run file TPR.
  • string
step23_grompp_nvt_config Config file Configuration file for biobb_gromacs.grompp tool.
  • string
step24_mdrun_nvt_output_trr_path Output file Path to the GROMACS uncompressed raw trajectory file TRR.
  • string
step24_mdrun_nvt_output_gro_path Output file Path to the output GROMACS structure GRO file.
  • string
step24_mdrun_nvt_output_edr_path Output file Path to the output GROMACS portable energy file EDR.
  • string
step24_mdrun_nvt_output_log_path Output file Path to the output GROMACS trajectory log file LOG.
  • string
step24_mdrun_nvt_output_cpt_path Output file Path to the output GROMACS checkpoint file CPT.
  • string
step25_gmx_energy_nvt_output_xvg_path Output file Path to the XVG output file.
  • string
step25_gmx_energy_nvt_config Config file Configuration file for biobb_analysis.gmx_energy tool.
  • string
step26_grompp_npt_output_tpr_path Output file Path to the output portable binary run file TPR.
  • string
step26_grompp_npt_config Config file Configuration file for biobb_gromacs.grompp tool.
  • string
step27_mdrun_npt_output_trr_path Output file Path to the GROMACS uncompressed raw trajectory file TRR.
  • string
step27_mdrun_npt_output_gro_path Output file Path to the output GROMACS structure GRO file.
  • string
step27_mdrun_npt_output_edr_path Output file Path to the output GROMACS portable energy file EDR.
  • string
step27_mdrun_npt_output_log_path Output file Path to the output GROMACS trajectory log file LOG.
  • string
step27_mdrun_npt_output_cpt_path Output file Path to the output GROMACS checkpoint file CPT.
  • string
step28_gmx_energy_npt_output_xvg_path Output file Path to the XVG output file.
  • string
step28_gmx_energy_npt_config Config file Configuration file for biobb_analysis.gmx_energy tool.
  • string
step29_grompp_md_output_tpr_path Output file Path to the output portable binary run file TPR.
  • string
step29_grompp_md_config Config file Configuration file for biobb_gromacs.grompp tool.
  • string
step30_mdrun_md_output_trr_path Output file Path to the GROMACS uncompressed raw trajectory file TRR.
  • string
step30_mdrun_md_output_gro_path Output file Path to the output GROMACS structure GRO file.
  • string
step30_mdrun_md_output_edr_path Output file Path to the output GROMACS portable energy file EDR.
  • string
step30_mdrun_md_output_log_path Output file Path to the output GROMACS trajectory log file LOG.
  • string
step30_mdrun_md_output_cpt_path Output file Path to the output GROMACS checkpoint file CPT.
  • string
step34_gmx_image_output_traj_path Output file Path to the output file.
  • string
step34_gmx_image_config Config file Configuration file for biobb_analysis.gmx_image tool.
  • string
step34b_gmx_image2_output_traj_path Output file Path to the output file.
  • string
step34b_gmx_image2_config Config file Configuration file for biobb_analysis.gmx_image tool.
  • string
step35_gmx_trjconv_str_output_str_path Output file Path to the output file.
  • string
step35_gmx_trjconv_str_config Config file Configuration file for biobb_analysis.gmx_trjconv_str tool.
  • string
step31_rmsd_first_output_xvg_path Output file Path to the XVG output file.
  • string
step31_rmsd_first_config Config file Configuration file for biobb_analysis.gmx_rms tool.
  • string
step32_rmsd_exp_output_xvg_path Output file Path to the XVG output file.
  • string
step32_rmsd_exp_config Config file Configuration file for biobb_analysis.gmx_rms tool.
  • string
step33_gmx_rgyr_output_xvg_path Output file Path to the XVG output file.
  • string
step33_gmx_rgyr_config Config file Configuration file for biobb_analysis.gmx_rgyr tool.
  • string
step36_grompp_md_output_tpr_path Output file Path to the output portable binary run file TPR.
  • string
step36_grompp_md_config Config file Configuration file for biobb_gromacs.grompp tool.
  • string

Steps

ID Name Description
step0_reduce_remove_hydrogens reduce_remove_hydrogens Removes hydrogen atoms to small molecules.
step2_extract_molecule extract_molecule This class is a wrapper of the Structure Checking tool to extract a molecule from a 3D structure.
step00_cat_pdb cat_pdb Class to concat two PDB structures in a single PDB file.
step4_fix_side_chain fix_side_chain Reconstructs the missing side chains and heavy atoms of the given PDB file.
step5_pdb2gmx pdb2gmx Creates a compressed (ZIP) GROMACS topology (TOP and ITP files) from a given PDB file.
step9_make_ndx make_ndx Creates a GROMACS index file (NDX) from an input selection and an input GROMACS structure file.
step10_genrestr genrestr Creates a new GROMACS compressed topology applying the indicated force restrains to the given input compressed topology.
step11_gmx_trjconv_str_protein gmx_trjconv_str Wrapper of the GROMACS trjconv module for converting between GROMACS compatible structure file formats and/or extracting a selection of atoms.
step12_gmx_trjconv_str_ligand gmx_trjconv_str Wrapper of the GROMACS trjconv module for converting between GROMACS compatible structure file formats and/or extracting a selection of atoms.
step13_cat_pdb_hydrogens cat_pdb Class to concat two PDB structures in a single PDB file.
step14_append_ligand append_ligand Takes a ligand ITP file and inserts it in a topology.
step15_editconf editconf Creates a GROMACS structure file (GRO) adding the information of the solvent box to the input structure file.
step16_solvate solvate Creates a new compressed GROMACS topology file adding solvent molecules to a given input compressed GROMACS topology file.
step17_grompp_genion grompp Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology.
step18_genion genion Creates a new compressed GROMACS topology adding ions until reaching the desired concentration to the input compressed GROMACS topology.
step19_grompp_min grompp Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology.
step20_mdrun_min mdrun Performs molecular dynamics simulations from an input GROMACS TPR file.
step21_gmx_energy_min gmx_energy Wrapper of the GROMACS energy module for extracting energy components from a given GROMACS energy file.
step22_make_ndx make_ndx Creates a GROMACS index file (NDX) from an input selection and an input GROMACS structure file.
step23_grompp_nvt grompp Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology.
step24_mdrun_nvt mdrun Performs molecular dynamics simulations from an input GROMACS TPR file.
step25_gmx_energy_nvt gmx_energy Wrapper of the GROMACS energy module for extracting energy components from a given GROMACS energy file.
step26_grompp_npt grompp Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology.
step27_mdrun_npt mdrun Performs molecular dynamics simulations from an input GROMACS TPR file.
step28_gmx_energy_npt gmx_energy Wrapper of the GROMACS energy module for extracting energy components from a given GROMACS energy file.
step29_grompp_md grompp Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology.
step30_mdrun_md mdrun Performs molecular dynamics simulations from an input GROMACS TPR file.
step34_gmx_image gmx_image Wrapper of the GROMACS trjconv module for correcting periodicity (image) from a given GROMACS compatible trajectory file.
step34b_gmx_image2 gmx_image Wrapper of the GROMACS trjconv module for correcting periodicity (image) from a given GROMACS compatible trajectory file.
step35_gmx_trjconv_str gmx_trjconv_str Wrapper of the GROMACS trjconv module for converting between GROMACS compatible structure file formats and/or extracting a selection of atoms.
step31_rmsd_first gmx_rms Wrapper of the GROMACS module for calculating the Root Mean Square deviation (RMSd) of a given GROMACS compatible trajectory.
step32_rmsd_exp gmx_rms Wrapper of the GROMACS module for calculating the Root Mean Square deviation (RMSd) of a given GROMACS compatible trajectory.
step33_gmx_rgyr gmx_rgyr 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.
step36_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
step2_extract_molecule_out1 output_molecule_path Output molecule file path.
  • File
step00_cat_pdb_out1 output_structure_path Output protein file path.
  • File
step4_fix_side_chain_out1 output_pdb_path Output PDB file path.
  • File
step5_pdb2gmx_out1 output_gro_path Path to the output GRO file.
  • File
step5_pdb2gmx_out2 output_top_zip_path Path the output TOP topology in zip format.
  • File
step9_make_ndx_out1 output_ndx_path Path to the output index NDX file.
  • File
step10_genrestr_out1 output_itp_path Path the output ITP topology file with restrains.
  • File
step11_gmx_trjconv_str_protein_out1 output_str_path Path to the output file.
  • File
step12_gmx_trjconv_str_ligand_out1 output_str_path Path to the output file.
  • File
step13_cat_pdb_hydrogens_out1 output_structure_path Output protein file path.
  • File
step14_append_ligand_out1 output_top_zip_path Path/Name the output topology TOP and ITP files zipball.
  • File
step15_editconf_out1 output_gro_path Path to the output GRO file.
  • File
step16_solvate_out1 output_gro_path Path to the output GRO file.
  • File
step16_solvate_out2 output_top_zip_path Path the output topology in zip format.
  • File
step17_grompp_genion_out1 output_tpr_path Path to the output portable binary run file TPR.
  • File
step18_genion_out1 output_gro_path Path to the input structure GRO file.
  • File
step18_genion_out2 output_top_zip_path Path the output topology TOP and ITP files zipball.
  • File
step19_grompp_min_out1 output_tpr_path Path to the output portable binary run file TPR.
  • File
step20_mdrun_min_out1 output_trr_path Path to the GROMACS uncompressed raw trajectory file TRR.
  • File
step20_mdrun_min_out2 output_gro_path Path to the output GROMACS structure GRO file.
  • File
step20_mdrun_min_out3 output_edr_path Path to the output GROMACS portable energy file EDR.
  • File
step20_mdrun_min_out4 output_log_path Path to the output GROMACS trajectory log file LOG.
  • File
step21_gmx_energy_min_out1 output_xvg_path Path to the XVG output file.
  • File
step22_make_ndx_out1 output_ndx_path Path to the output index NDX file.
  • File
step23_grompp_nvt_out1 output_tpr_path Path to the output portable binary run file TPR.
  • File
step24_mdrun_nvt_out1 output_trr_path Path to the GROMACS uncompressed raw trajectory file TRR.
  • File
step24_mdrun_nvt_out2 output_gro_path Path to the output GROMACS structure GRO file.
  • File
step24_mdrun_nvt_out3 output_edr_path Path to the output GROMACS portable energy file EDR.
  • File
step24_mdrun_nvt_out4 output_log_path Path to the output GROMACS trajectory log file LOG.
  • File
step24_mdrun_nvt_out5 output_cpt_path Path to the output GROMACS checkpoint file CPT.
  • File
step25_gmx_energy_nvt_out1 output_xvg_path Path to the XVG output file.
  • File
step26_grompp_npt_out1 output_tpr_path Path to the output portable binary run file TPR.
  • File
step27_mdrun_npt_out1 output_trr_path Path to the GROMACS uncompressed raw trajectory file TRR.
  • File
step27_mdrun_npt_out2 output_gro_path Path to the output GROMACS structure GRO file.
  • File
step27_mdrun_npt_out3 output_edr_path Path to the output GROMACS portable energy file EDR.
  • File
step27_mdrun_npt_out4 output_log_path Path to the output GROMACS trajectory log file LOG.
  • File
step27_mdrun_npt_out5 output_cpt_path Path to the output GROMACS checkpoint file CPT.
  • File
step28_gmx_energy_npt_out1 output_xvg_path Path to the XVG output file.
  • File
step29_grompp_md_out1 output_tpr_path Path to the output portable binary run file TPR.
  • File
step30_mdrun_md_out1 output_trr_path Path to the GROMACS uncompressed raw trajectory file TRR.
  • File
step30_mdrun_md_out2 output_gro_path Path to the output GROMACS structure GRO file.
  • File
step30_mdrun_md_out3 output_edr_path Path to the output GROMACS portable energy file EDR.
  • File
step30_mdrun_md_out4 output_log_path Path to the output GROMACS trajectory log file LOG.
  • File
step30_mdrun_md_out5 output_cpt_path Path to the output GROMACS checkpoint file CPT.
  • File
step34_gmx_image_out1 output_traj_path Path to the output file.
  • File
step34b_gmx_image2_out1 output_traj_path Path to the output file.
  • File
step35_gmx_trjconv_str_out1 output_str_path Path to the output file.
  • File
step31_rmsd_first_out1 output_xvg_path Path to the XVG output file.
  • File
step32_rmsd_exp_out1 output_xvg_path Path to the XVG output file.
  • File
step33_gmx_rgyr_out1 output_xvg_path Path to the XVG output file.
  • File
step36_grompp_md_out1 output_tpr_path Path to the output portable binary run file TPR.
  • File

Version History

Version 2 (latest) Created 7th Jun 2023 at 11:54 by Genís Bayarri

Updated workflow descriptors


Frozen Version-2 b82813d

Version 1 (earliest) Created 10th Jan 2022 at 11:52 by Genís Bayarri

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Frozen Version-1 2816c50
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Citation
Hospital, A., & Bayarri, G. (2023). CWL Protein Ligand Complex MD Setup tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.258.2
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Created: 10th Jan 2022 at 11:52

Last updated: 17th Mar 2022 at 09:54

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