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.

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 MakeNdx biobb_gromacs_make_ndx_ext
21 GmxEnergy Min biobb_analysis_gmx_energy_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 Type
mypdb_prot.pdb mypdb_prot.pdb n/a
  • File
myextract_heteroatoms.pdb myextract_heteroatoms.pdb n/a
  • File
myextract_molecule.pdb myextract_molecule.pdb n/a
  • File
myreduce_add_hydrogens.pdb myreduce_add_hydrogens.pdb n/a
  • File
myfix_side_chain.pdb myfix_side_chain.pdb n/a
  • File
mybabel_minimize.mol2 mybabel_minimize.mol2 n/a
  • File
mypdb2gmx.zip mypdb2gmx.zip n/a
  • File
mypdb2gmx.gro mypdb2gmx.gro n/a
  • File
myacpype_params_gmx.itp myacpype_params_gmx.itp n/a
  • File
myacpype_params_gmx.gro myacpype_params_gmx.gro n/a
  • File
myacpype_params_gmx.top myacpype_params_gmx.top n/a
  • File
mygmx_trjconv_str_prot.pdb mygmx_trjconv_str_prot.pdb n/a
  • File
mymake_ndx.ndx mymake_ndx.ndx n/a
  • File
mygmx_trjconv_str_lig.pdb mygmx_trjconv_str_lig.pdb n/a
  • File
mygenrestr.itp mygenrestr.itp n/a
  • File
mycat_pdb.pdb mycat_pdb.pdb n/a
  • File
myappend_ligand.zip myappend_ligand.zip n/a
  • File
myeditconf.gro myeditconf.gro n/a
  • File
mysolvate.gro mysolvate.gro n/a
  • File
mysolvate.zip mysolvate.zip n/a
  • File
mygrompp_ion.tpr mygrompp_ion.tpr n/a
  • File
mygenion.gro mygenion.gro n/a
  • File
mygenion.zip mygenion.zip n/a
  • File
_anonymous_output_1 _anonymous_output_1 n/a
  • File
mymdrun.edr mymdrun.edr n/a
  • File
mymdrun.log mymdrun.log n/a
  • File
mymdrun.cpt mymdrun.cpt n/a
  • File
mymdrun.xvg mymdrun.xvg n/a
  • File
mymdrun.trr mymdrun.trr n/a
  • File
mymdrun.gro mymdrun.gro n/a
  • File
mymdrun.xtc mymdrun.xtc n/a
  • File
_anonymous_output_2 _anonymous_output_2 n/a
  • File
mygmx_energy.xvg mygmx_energy.xvg n/a
  • File
_anonymous_output_3 _anonymous_output_3 n/a
  • File
_anonymous_output_4 _anonymous_output_4 n/a
  • File
_anonymous_output_5 _anonymous_output_5 n/a
  • File
_anonymous_output_6 _anonymous_output_6 n/a
  • File
_anonymous_output_7 _anonymous_output_7 n/a
  • File
_anonymous_output_8 _anonymous_output_8 n/a
  • File
_anonymous_output_9 _anonymous_output_9 n/a
  • File
_anonymous_output_10 _anonymous_output_10 n/a
  • File
_anonymous_output_11 _anonymous_output_11 n/a
  • File
_anonymous_output_12 _anonymous_output_12 n/a
  • File
_anonymous_output_13 _anonymous_output_13 n/a
  • File
_anonymous_output_14 _anonymous_output_14 n/a
  • File
_anonymous_output_15 _anonymous_output_15 n/a
  • File
_anonymous_output_16 _anonymous_output_16 n/a
  • File
_anonymous_output_17 _anonymous_output_17 n/a
  • File
_anonymous_output_18 _anonymous_output_18 n/a
  • File
_anonymous_output_19 _anonymous_output_19 n/a
  • File
_anonymous_output_20 _anonymous_output_20 n/a
  • File
_anonymous_output_21 _anonymous_output_21 n/a
  • File
_anonymous_output_22 _anonymous_output_22 n/a
  • File
_anonymous_output_23 _anonymous_output_23 n/a
  • File
_anonymous_output_24 _anonymous_output_24 n/a
  • File
_anonymous_output_25 _anonymous_output_25 n/a
  • File
_anonymous_output_26 _anonymous_output_26 n/a
  • File
_anonymous_output_27 _anonymous_output_27 n/a
  • File
_anonymous_output_28 _anonymous_output_28 n/a
  • File
mygmx_rgyr.xvg mygmx_rgyr.xvg n/a
  • File
_anonymous_output_29 _anonymous_output_29 n/a
  • File
mygmx_rms_exp.xvg mygmx_rms_exp.xvg n/a
  • File
_anonymous_output_30 _anonymous_output_30 n/a
  • File
mygmx_image.trr mygmx_image.trr n/a
  • File

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 2 Created 22nd Nov 2022 at 09:57 by Genís Bayarri

No revision comments

Open master 4b22d97

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

Initial commit


Frozen Version-1 779961b
help Creators and Submitter
Citation
Hospital, A., & Bayarri, G. (2023). Galaxy Protein Ligand Complex MD Setup. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.295.3
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Created: 24th Mar 2022 at 14:47

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