Workflow Type: Galaxy
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Protein 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, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).
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) 2015-2023 Barcelona Supercomputing Center
- (c) 2015-2023 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 | FixSideChain | biobb_model_fix_side_chain_ext |
2 | Pdb2gmx | biobb_gromacs_pdb2gmx_ext |
3 | Editconf | biobb_gromacs_editconf_ext |
4 | Solvate | biobb_gromacs_solvate_ext |
5 | Grompp Ion | biobb_gromacs_grompp_ext |
6 | Genion | biobb_gromacs_genion_ext |
7 | Grompp Min | biobb_gromacs_grompp_ext |
8 | Mdrun Min | biobb_gromacs_mdrun_ext |
9 | Grompp NVT | biobb_gromacs_grompp_ext |
10 | GmxEnergy Min | biobb_analysis_gmx_energy_ext |
11 | Mdrun NVT | biobb_gromacs_mdrun_ext |
12 | Grompp NPT | biobb_gromacs_grompp_ext |
13 | GmxEnergy NVT | biobb_analysis_gmx_energy_ext |
14 | Mdrun NPT | biobb_gromacs_mdrun_ext |
15 | Free Grompp | biobb_gromacs_grompp_ext |
16 | GmxEnergy NPT | biobb_analysis_gmx_energy_ext |
17 | Free Mdrun | biobb_gromacs_mdrun_ext |
18 | GmxRms Exp | biobb_analysis_gmx_rms_ext |
19 | GmxRms | biobb_analysis_gmx_rms_ext |
20 | GmxRgyr | biobb_analysis_gmx_rgyr_ext |
21 | GmxImage | biobb_analysis_gmx_image_ext |
22 | GmxTrjconvStr | biobb_analysis_gmx_trjconv_str_ext |
Outputs
ID | Name | Description | Type |
---|---|---|---|
mypdb.pdb | mypdb.pdb | n/a |
|
myfix_side_chain.pdb | myfix_side_chain.pdb | n/a |
|
mypdb2gmx.gro | mypdb2gmx.gro | n/a |
|
mypdb2gmx.zip | mypdb2gmx.zip | n/a |
|
myeditconf.pdb | myeditconf.pdb | n/a |
|
mysolvate.gro | mysolvate.gro | n/a |
|
mysolvate.zip | mysolvate.zip | n/a |
|
mygrompp.tpr | mygrompp.tpr | n/a |
|
mygenion.zip | mygenion.zip | n/a |
|
mygenion.gro | mygenion.gro | n/a |
|
_anonymous_output_1 | _anonymous_output_1 | n/a |
|
mymdrun.xtc | mymdrun.xtc | n/a |
|
mymdrun.log | mymdrun.log | n/a |
|
mymdrun.cpt | mymdrun.cpt | n/a |
|
mymdrun.xvg | mymdrun.xvg | n/a |
|
mymdrun.gro | mymdrun.gro | n/a |
|
mymdrun.edr | mymdrun.edr | n/a |
|
mymdrun.trr | mymdrun.trr | n/a |
|
_anonymous_output_2 | _anonymous_output_2 | n/a |
|
mygmx_energy.xvg | mygmx_energy.xvg | 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 |
|
_anonymous_output_22 | _anonymous_output_22 | n/a |
|
_anonymous_output_23 | _anonymous_output_23 | n/a |
|
_anonymous_output_24 | _anonymous_output_24 | n/a |
|
_anonymous_output_25 | _anonymous_output_25 | n/a |
|
_anonymous_output_26 | _anonymous_output_26 | n/a |
|
_anonymous_output_27 | _anonymous_output_27 | n/a |
|
_anonymous_output_28 | _anonymous_output_28 | n/a |
|
mygmx_rms.xvg | mygmx_rms.xvg | n/a |
|
mygmx_rgyr.xvg | mygmx_rgyr.xvg | n/a |
|
mygmx_image.xtc | mygmx_image.xtc | n/a |
|
mygmx_trjconv_str.pdb | mygmx_trjconv_str.pdb | n/a |
|
Version History
Version 3 (latest) Created 3rd May 2023 at 14:41 by Genís Bayarri
Update to BioBB 4.0.*
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Version-3
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Version 2 Created 22nd Nov 2022 at 09:46 by Genís Bayarri
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Version-2
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Version 1 (earliest) Created 14th Mar 2022 at 10:15 by Genís Bayarri
Initial commit
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e55fd41
Creators and Submitter
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Citation
Hospital, A., & Bayarri, G. (2023). Galaxy Protein MD Setup tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.277.3
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Views: 4401 Downloads: 709 Runs: 0
Created: 14th Mar 2022 at 10:15
Last updated: 3rd May 2023 at 14:41
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