Galaxy Protein Ligand Complex MD Setup
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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.

SEEK ID: https://workflowhub.eu/workflows/295?version=2

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_gromacs_pdb2gmx_ext
7	AcpypeParamsGmx	biobb_chemistry_acpype_params_gmx_ext
8	GmxTrjconvStr	biobb_analysis_gmx_trjconv_str_ext
9	MakeNdx	biobb_gromacs_make_ndx_ext
10	GmxTrjconvStr	biobb_analysis_gmx_trjconv_str_ext
11	Genrestr	biobb_gromacs_genrestr_ext
12	CatPdb	biobb_structure_utils_cat_pdb_ext
13	AppendLigand	biobb_gromacs_append_ligand_ext
14	Editconf	biobb_gromacs_editconf_ext
15	Solvate	biobb_gromacs_solvate_ext
16	Grompp Ion	biobb_gromacs_grompp_ext
17	Genion	biobb_gromacs_genion_ext
18	Grompp Min	biobb_gromacs_grompp_ext
19	Mdrun Min	biobb_gromacs_mdrun_ext
20	GmxEnergy Min	biobb_analysis_gmx_energy_ext
21	MakeNdx	biobb_gromacs_make_ndx_ext
22	Grompp NVT	biobb_gromacs_grompp_ext
23	Mdrun NVT	biobb_gromacs_mdrun_ext
24	GmxEnergy NVT	biobb_analysis_gmx_energy_ext
25	Grompp NPT	biobb_gromacs_grompp_ext
26	Mdrun NPT	biobb_gromacs_mdrun_ext
27	GmxEnergy NPT	biobb_analysis_gmx_energy_ext
28	Grompp MD	biobb_gromacs_grompp_ext
29	Mdrun MD	biobb_gromacs_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
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