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).
- (c) 2015-2022 Barcelona Supercomputing Center
- (c) 2015-2022 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
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 |
---|---|---|---|
mypdb_prot.pdb | mypdb_prot.pdb | n/a |
|
myextract_heteroatoms.pdb | myextract_heteroatoms.pdb | n/a |
|
myextract_molecule.pdb | myextract_molecule.pdb | n/a |
|
myreduce_add_hydrogens.pdb | myreduce_add_hydrogens.pdb | n/a |
|
myfix_side_chain.pdb | myfix_side_chain.pdb | n/a |
|
mybabel_minimize.mol2 | mybabel_minimize.mol2 | n/a |
|
mypdb2gmx.zip | mypdb2gmx.zip | n/a |
|
mypdb2gmx.gro | mypdb2gmx.gro | n/a |
|
myacpype_params_gmx.gro | myacpype_params_gmx.gro | n/a |
|
myacpype_params_gmx.itp | myacpype_params_gmx.itp | n/a |
|
myacpype_params_gmx.top | myacpype_params_gmx.top | n/a |
|
mygmx_trjconv_str_prot.pdb | mygmx_trjconv_str_prot.pdb | n/a |
|
mymake_ndx.ndx | mymake_ndx.ndx | n/a |
|
mygmx_trjconv_str_lig.pdb | mygmx_trjconv_str_lig.pdb | n/a |
|
mygenrestr.itp | mygenrestr.itp | n/a |
|
mycat_pdb.pdb | mycat_pdb.pdb | n/a |
|
myappend_ligand.zip | myappend_ligand.zip | n/a |
|
myeditconf.gro | myeditconf.gro | n/a |
|
mysolvate.zip | mysolvate.zip | n/a |
|
mysolvate.gro | mysolvate.gro | n/a |
|
mygrompp_ion.tpr | mygrompp_ion.tpr | n/a |
|
mygenion.gro | mygenion.gro | n/a |
|
mygenion.zip | mygenion.zip | n/a |
|
_anonymous_output_1 | _anonymous_output_1 | n/a |
|
mymdrun.edr | mymdrun.edr | n/a |
|
mymdrun.log | mymdrun.log | n/a |
|
mymdrun.xtc | mymdrun.xtc | n/a |
|
mymdrun.cpt | mymdrun.cpt | n/a |
|
mymdrun.xvg | mymdrun.xvg | n/a |
|
mymdrun.trr | mymdrun.trr | n/a |
|
mymdrun.gro | mymdrun.gro | n/a |
|
mygmx_energy.xvg | mygmx_energy.xvg | n/a |
|
_anonymous_output_2 | _anonymous_output_2 | n/a |
|
_anonymous_output_3 | _anonymous_output_3 | n/a |
|
_anonymous_output_4 | _anonymous_output_4 | n/a |
|
_anonymous_output_5 | _anonymous_output_5 | n/a |
|
_anonymous_output_6 | _anonymous_output_6 | n/a |
|
_anonymous_output_7 | _anonymous_output_7 | n/a |
|
_anonymous_output_8 | _anonymous_output_8 | n/a |
|
_anonymous_output_9 | _anonymous_output_9 | n/a |
|
_anonymous_output_10 | _anonymous_output_10 | n/a |
|
_anonymous_output_11 | _anonymous_output_11 | n/a |
|
_anonymous_output_12 | _anonymous_output_12 | n/a |
|
_anonymous_output_13 | _anonymous_output_13 | n/a |
|
_anonymous_output_14 | _anonymous_output_14 | n/a |
|
_anonymous_output_15 | _anonymous_output_15 | n/a |
|
_anonymous_output_16 | _anonymous_output_16 | n/a |
|
_anonymous_output_17 | _anonymous_output_17 | n/a |
|
_anonymous_output_18 | _anonymous_output_18 | n/a |
|
_anonymous_output_19 | _anonymous_output_19 | n/a |
|
_anonymous_output_20 | _anonymous_output_20 | n/a |
|
_anonymous_output_21 | _anonymous_output_21 | n/a |
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_anonymous_output_22 | _anonymous_output_22 | n/a |
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_anonymous_output_23 | _anonymous_output_23 | n/a |
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_anonymous_output_24 | _anonymous_output_24 | n/a |
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_anonymous_output_25 | _anonymous_output_25 | n/a |
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_anonymous_output_26 | _anonymous_output_26 | n/a |
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_anonymous_output_27 | _anonymous_output_27 | n/a |
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_anonymous_output_28 | _anonymous_output_28 | n/a |
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mygmx_rgyr.xvg | mygmx_rgyr.xvg | n/a |
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_anonymous_output_29 | _anonymous_output_29 | n/a |
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mygmx_rms_exp.xvg | mygmx_rms_exp.xvg | n/a |
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_anonymous_output_30 | _anonymous_output_30 | n/a |
|
mygmx_image.trr | mygmx_image.trr | n/a |
|
Version History
Version 3 (latest) Created 3rd May 2023 at 14:46 by Genís Bayarri
Update to BioBB 4.0.*
Frozen
Version-3
f82202f
Version 1 (earliest) Created 24th Mar 2022 at 14:47 by Genís Bayarri
Initial commit
Frozen
Version-1
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Creators
Submitter
Views: 3755 Downloads: 591 Runs: 0
Created: 24th Mar 2022 at 14:47
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