Workflow Type: Galaxy
Open
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.
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 |
|
myfix_side_chain.pdb | myfix_side_chain.pdb | n/a |
|
mypdb2gmx.gro | mypdb2gmx.gro | n/a |
|
mypdb2gmx.zip | mypdb2gmx.zip | n/a |
|
myeditconf.gro | myeditconf.gro | n/a |
|
mysolvate.zip | mysolvate.zip | n/a |
|
mysolvate.gro | mysolvate.gro | n/a |
|
mygrompp.tpr | mygrompp.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 |
|
_anonymous_output_2 | _anonymous_output_2 | n/a |
|
energy_min.xvg | energy_min.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 |
|
energy_nvt.xvg | energy_nvt.xvg | n/a |
|
_anonymous_output_11 | _anonymous_output_11 | n/a |
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_anonymous_output_12 | _anonymous_output_12 | n/a |
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_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 |
|
energy_npt.xvg | energy_npt.xvg | n/a |
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_anonymous_output_19 | _anonymous_output_19 | n/a |
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_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 |
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rmsd_first.xvg | rmsd_first.xvg | n/a |
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mygmx_image.xtc | mygmx_image.xtc | n/a |
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mygmx_trjconv_str.xtc | mygmx_trjconv_str.xtc | n/a |
|
rmsd_exp.xvg | rmsd_exp.xvg | n/a |
|
mygmx_rgyr.xvg | mygmx_rgyr.xvg | n/a |
|
Version History
Version 1 (earliest) Created 26th Sep 2021 at 20:50 by Douglas Lowe
Added/updated 1 files
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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
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Views: 3895 Downloads: 283 Runs: 2
Created: 26th Sep 2021 at 20:50
Last updated: 10th Feb 2022 at 16:22
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