Galaxy Protein Ligand Complex MD Setup
Version 1

Workflow Type: Galaxy
Stable

Protein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb)


This workflow must be run in biobb.usegalaxy.es. Please, click here to access.


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.

Inputs

ID Name Description Type
input_index_path input_index_path runtime parameter for tool GmxTrjconvStr n/a
input_ndx_path input_ndx_path runtime parameter for tool MakeNdx n/a
input_index_path input_index_path runtime parameter for tool GmxTrjconvStr n/a
input_solvent_gro_path input_solvent_gro_path runtime parameter for tool Solvate n/a
input_cpt_path input_cpt_path runtime parameter for tool Grompp n/a
input_mdp_path input_mdp_path runtime parameter for tool Grompp n/a
input_ndx_path input_ndx_path runtime parameter for tool Grompp n/a
input_ndx_path input_ndx_path runtime parameter for tool Genion n/a
input_cpt_path input_cpt_path runtime parameter for tool Grompp n/a
input_mdp_path input_mdp_path runtime parameter for tool Grompp n/a
input_ndx_path input_ndx_path runtime parameter for tool Grompp n/a
input_cpt_path input_cpt_path runtime parameter for tool Mdrun n/a
input_ndx_path input_ndx_path runtime parameter for tool MakeNdx n/a
input_cpt_path input_cpt_path runtime parameter for tool Grompp n/a
input_mdp_path input_mdp_path runtime parameter for tool Grompp n/a
input_cpt_path input_cpt_path runtime parameter for tool Mdrun n/a
input_mdp_path input_mdp_path runtime parameter for tool Grompp n/a
input_cpt_path input_cpt_path runtime parameter for tool Mdrun n/a
input_mdp_path input_mdp_path runtime parameter for tool Grompp n/a
input_ndx_path input_ndx_path runtime parameter for tool Grompp n/a
input_cpt_path input_cpt_path runtime parameter for tool Mdrun n/a
input_index_path input_index_path runtime parameter for tool GmxRgyr n/a
input_index_path input_index_path runtime parameter for tool GmxRms n/a
input_index_path input_index_path runtime parameter for tool GmxRms n/a

Steps

ID Name Description
0 Pdb biobb_io_pdb_ext
1 ExtractHeteroatoms biobb_structure_utils_extract_heteroatoms_ext
2 ExtractMolecule biobb_structure_utils_extract_molecule_ext
3 ReduceAddHydrogens biobb_chemistry_reduce_add_hydrogens_ext
4 FixSideChain biobb_model_fix_side_chain_ext
5 BabelMinimize biobb_chemistry_babel_minimize_ext
6 Pdb2gmx biobb_md_pdb2gmx_ext
7 AcpypeParamsGmx biobb_chemistry_acpype_params_gmx_ext
8 GmxTrjconvStr biobb_analysis_gmx_trjconv_str_ext
9 MakeNdx biobb_md_make_ndx_ext
10 GmxTrjconvStr biobb_analysis_gmx_trjconv_str_ext
11 Genrestr biobb_md_genrestr_ext
12 CatPdb biobb_structure_utils_cat_pdb_ext
13 AppendLigand biobb_md_append_ligand_ext
14 Editconf biobb_md_editconf_ext
15 Solvate biobb_md_solvate_ext
16 Grompp Ion biobb_md_grompp_ext
17 Genion biobb_md_genion_ext
18 Grompp Min biobb_md_grompp_ext
19 Mdrun Min biobb_md_mdrun_ext
20 GmxEnergy Min biobb_analysis_gmx_energy_ext
21 MakeNdx biobb_md_make_ndx_ext
22 Grompp NVT biobb_md_grompp_ext
23 Mdrun NVT biobb_md_mdrun_ext
24 GmxEnergy NVT biobb_analysis_gmx_energy_ext
25 Grompp NPT biobb_md_grompp_ext
26 Mdrun NPT biobb_md_mdrun_ext
27 GmxEnergy NPT biobb_analysis_gmx_energy_ext
28 Grompp MD biobb_md_grompp_ext
29 Mdrun MD biobb_md_mdrun_ext
30 GmxRgyr biobb_analysis_gmx_rgyr_ext
31 GmxRms Exp. biobb_analysis_gmx_rms_ext
32 GmxRms biobb_analysis_gmx_rms_ext
33 GmxTrjconvStr biobb_analysis_gmx_trjconv_str_ext
34 GmxImage biobb_analysis_gmx_image_ext

Outputs

ID Name Description Type
output_pdb_path output_pdb_path n/a
output_heteroatom_path output_heteroatom_path n/a
output_molecule_path output_molecule_path n/a
output_path output_path n/a
output_pdb_path output_pdb_path n/a
output_path output_path n/a
output_gro_path output_gro_path n/a
output_top_zip_path output_top_zip_path n/a
output_path_gro output_path_gro n/a
output_path_itp output_path_itp n/a
output_path_top output_path_top n/a
output_str_path output_str_path n/a
output_ndx_path output_ndx_path n/a
output_str_path output_str_path n/a
output_itp_path output_itp_path n/a
output_structure_path output_structure_path n/a
output_top_zip_path output_top_zip_path n/a
output_gro_path output_gro_path n/a
output_gro_path output_gro_path n/a
output_top_zip_path output_top_zip_path n/a
output_tpr_path output_tpr_path n/a
output_gro_path output_gro_path n/a
output_top_zip_path output_top_zip_path n/a
output_tpr_path output_tpr_path n/a
output_trr_path output_trr_path n/a
output_gro_path output_gro_path n/a
output_edr_path output_edr_path n/a
output_log_path output_log_path n/a
output_xtc_path output_xtc_path n/a
output_cpt_path output_cpt_path n/a
output_dhdl_path output_dhdl_path n/a
output_xvg_path output_xvg_path n/a
output_ndx_path output_ndx_path n/a
output_tpr_path output_tpr_path n/a
output_trr_path output_trr_path n/a
output_gro_path output_gro_path n/a
output_edr_path output_edr_path n/a
output_log_path output_log_path n/a
output_xtc_path output_xtc_path n/a
output_cpt_path output_cpt_path n/a
output_dhdl_path output_dhdl_path n/a
output_xvg_path output_xvg_path n/a
output_tpr_path output_tpr_path n/a
output_trr_path output_trr_path n/a
output_gro_path output_gro_path n/a
output_edr_path output_edr_path n/a
output_log_path output_log_path n/a
output_xtc_path output_xtc_path n/a
output_cpt_path output_cpt_path n/a
output_dhdl_path output_dhdl_path n/a
output_xvg_path output_xvg_path n/a
output_tpr_path output_tpr_path n/a
output_trr_path output_trr_path n/a
output_gro_path output_gro_path n/a
output_edr_path output_edr_path n/a
output_log_path output_log_path n/a
output_xtc_path output_xtc_path n/a
output_cpt_path output_cpt_path n/a
output_dhdl_path output_dhdl_path n/a
output_xvg_path output_xvg_path n/a
output_xvg_path output_xvg_path n/a
output_xvg_path output_xvg_path n/a
output_str_path output_str_path n/a
output_traj_path output_traj_path n/a

Version History

Version 1 (earliest) Created 24th Mar 2022 at 14:47 by Genís Bayarri

Initial commit


Open master 779961b
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Views: 186

Created: 24th Mar 2022 at 14:47

Last used: 28th Jun 2022 at 16:06

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