Protein MD Setup tutorial using BioExcel Building Blocks (biobb) in Galaxy
Version 1

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Workflow Type: Galaxy
Work-in-progress

Galaxy workflow example that 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). This workflow returns a resulting protein structure and simulated 3D trajectories.

Designed for running on the https://dev.usegalaxy.es Galaxy instance.

SEEK ID: https://workflowhub.eu/workflows/194?version=1

DOI: 10.48546/workflowhub.workflow.194.1

Steps

ID Name Description
0 step1_pdb Download a protein structure from the PDB database biobb_io_pdb_ext
1 step2_fixsidechain Fix the side chains, adding any side chain atoms missing in the original structure biobb_model_fix_side_chain_ext
2 step3_pdb2gmx Create Protein System Topology biobb_md_pdb2gmx_ext
3 step4_editconf Create Solvent Box biobb_md_editconf_ext
4 step5_solvate Fill the box with water molecules biobb_md_solvate_ext
5 step6_grompp_genion Add Ions - part 1 biobb_md_grompp_ext
6 step7_genion Add Ions - part 2 biobb_md_genion_ext
7 step8_grompp_min Energetically minimize the system - part 1 biobb_md_grompp_ext
8 step9_mdrun_min Energetically minimize the system - part 2 biobb_md_mdrun_ext
9 step11_grompp_nvt Equilibriate the system (NVT) - part 1 biobb_md_grompp_ext
10 step10_energy_min Energetically minimize the system - part 3 biobb_analysis_gmx_energy_ext
11 step12_mdrun_nvt Equilibrate the system (NVT) - part 2 biobb_md_mdrun_ext
12 step14_grompp_npt Equilibrate the system (NPT) - part 1 biobb_md_grompp_ext
13 step13_energy_nvt Equilibrate the system (NVT) - part 3 biobb_analysis_gmx_energy_ext
14 step15_mdrun_npt Equilibrate the system (NPT) - part 2 biobb_md_mdrun_ext
15 step17_grompp_md Free molecular dynamics simulation - part 1 biobb_md_grompp_ext
16 step16_energy_npt Equilibrate the system (NPT) - part 3 biobb_analysis_gmx_energy_ext
17 step18_mdrun_md Free molecular dynamics simulation - part 2 biobb_md_mdrun_ext
18 step19_rmsfirst Post-processing resulting 3D trajectory - part 1 biobb_analysis_gmx_rms_ext
19 step22_image Post-processing resulting 3D trajectory - part 4 biobb_analysis_gmx_image_ext
20 step23_dry Post-processing resulting 3D trajectory - part 5 biobb_analysis_gmx_trjconv_str_ext
21 step20_rmsexp Post-processing resulting 3D trajectory - part 2 biobb_analysis_gmx_rms_ext
22 step21_rgyr Post-processing resulting 3D trajectory - part 3 biobb_analysis_gmx_rgyr_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.gro myeditconf.gro n/a
  • File
mysolvate.zip mysolvate.zip n/a
  • File
mysolvate.gro mysolvate.gro n/a
  • File
mygrompp.tpr mygrompp.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.xtc mymdrun.xtc 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
_anonymous_output_2 _anonymous_output_2 n/a
  • File
energy_min.xvg energy_min.xvg n/a
  • File
_anonymous_output_3 _anonymous_output_3 n/a
  • File
_anonymous_output_4 _anonymous_output_4 n/a
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_anonymous_output_5 _anonymous_output_5 n/a
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_anonymous_output_6 _anonymous_output_6 n/a
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_anonymous_output_7 _anonymous_output_7 n/a
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_anonymous_output_8 _anonymous_output_8 n/a
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_anonymous_output_9 _anonymous_output_9 n/a
  • File
_anonymous_output_10 _anonymous_output_10 n/a
  • File
energy_nvt.xvg energy_nvt.xvg n/a
  • File
_anonymous_output_11 _anonymous_output_11 n/a
  • File
_anonymous_output_12 _anonymous_output_12 n/a
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_anonymous_output_13 _anonymous_output_13 n/a
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_anonymous_output_14 _anonymous_output_14 n/a
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_anonymous_output_15 _anonymous_output_15 n/a
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_anonymous_output_16 _anonymous_output_16 n/a
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_anonymous_output_17 _anonymous_output_17 n/a
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_anonymous_output_18 _anonymous_output_18 n/a
  • File
energy_npt.xvg energy_npt.xvg n/a
  • File
_anonymous_output_19 _anonymous_output_19 n/a
  • File
_anonymous_output_20 _anonymous_output_20 n/a
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_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
  • File
rmsd_first.xvg rmsd_first.xvg n/a
  • File
mygmx_image.xtc mygmx_image.xtc n/a
  • File
mygmx_trjconv_str.xtc mygmx_trjconv_str.xtc n/a
  • File
rmsd_exp.xvg rmsd_exp.xvg n/a
  • File
mygmx_rgyr.xvg mygmx_rgyr.xvg n/a
  • File

Version History

Version 1 (earliest) Created 26th Sep 2021 at 20:50 by Douglas Lowe

Added/updated 1 files


Open master 13d1914
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Citation
Lowe, D. (2021). Protein MD Setup tutorial using BioExcel Building Blocks (biobb). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.194.1
License
Apache License 2.0
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Views: 4022   Downloads: 303   Runs: 2

Created: 26th Sep 2021 at 20:50

Last updated: 10th Feb 2022 at 16:22

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