Workflow Type: Galaxy
Stable

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).

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
  • File
myfix_side_chain.pdb myfix_side_chain.pdb n/a
  • File
mypdb2gmx.gro mypdb2gmx.gro n/a
  • File
mypdb2gmx.zip mypdb2gmx.zip n/a
  • File
myeditconf.pdb myeditconf.pdb n/a
  • File
mysolvate.gro mysolvate.gro n/a
  • File
mysolvate.zip mysolvate.zip n/a
  • File
mygrompp.tpr mygrompp.tpr n/a
  • File
mygenion.zip mygenion.zip n/a
  • File
mygenion.gro mygenion.gro n/a
  • File
_anonymous_output_1 _anonymous_output_1 n/a
  • File
mymdrun.xtc mymdrun.xtc 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.gro mymdrun.gro n/a
  • File
mymdrun.edr mymdrun.edr n/a
  • File
mymdrun.trr mymdrun.trr 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_rms.xvg mygmx_rms.xvg n/a
  • File
mygmx_rgyr.xvg mygmx_rgyr.xvg n/a
  • File
mygmx_image.xtc mygmx_image.xtc n/a
  • File
mygmx_trjconv_str.pdb mygmx_trjconv_str.pdb n/a
  • File

Version History

Version 3 (latest) Created 3rd May 2023 at 14:41 by Genís Bayarri

Update to BioBB 4.0.*


Frozen Version-3 3dbb764

Version 2 Created 22nd Nov 2022 at 09:46 by Genís Bayarri

No revision comments

Frozen Version-2 7703166

Version 1 (earliest) Created 14th Mar 2022 at 10:15 by Genís Bayarri

Initial commit


Frozen Version-1 e55fd41
help Creators and Submitter
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: 2917

Created: 14th Mar 2022 at 10:15

Last updated: 3rd May 2023 at 14:41

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