MD protein-ligand workflow (from PDB structure) 2.0
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Run on GalaxyHigh Throughput Molecular Dynamics and Analysis
Associated Tutorial
This workflows is part of the tutorial High Throughput Molecular Dynamics and Analysis, available in the GTN
Thanks to...
Tutorial Author(s): Simon Bray, Tharindu Senapathi, Christopher Barnett, Björn Grüning
Tutorial Contributor(s): Helena Rasche, Nadia Goué, Saskia Hiltemann, Simon Bray, Simon Gladman, Christopher Barnett, Tharindu Senapathi, Stéphanie Robin, Anthony Bretaudeau, Martin Čech, Björn Grüning, Armin Dadras
Funder(s): ELIXIR Europe, de.NBI, University of Freiburg
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Ligand name (e.g. AG5E) | Ligand name (e.g. AG5E) | n/a |
|
| PDB code (e.g. 6hhr) | PDB code (e.g. 6hhr) | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | Get PDB file | toolshed.g2.bx.psu.edu/repos/bgruening/get_pdb/get_pdb/0.1.0 |
| 3 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 |
| 4 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 |
| 5 | GROMACS initial setup | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2019.1.4 |
| 6 | Compound conversion | toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/2.4.2.2.0 |
| 7 | Generate MD topologies for small molecules | toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_acpype/ambertools_acpype/19.11 |
| 8 | Merge GROMACS topologies | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_merge_topology_files/gmx_merge_topology_files/3.2.0 |
| 9 | GROMACS structure configuration | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2019.1.4 |
| 10 | GROMACS solvation and adding ions | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2019.1.4 |
| 11 | GROMACS energy minimization | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2019.1.4 |
| 12 | GROMACS simulation | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.4.1 |
| 13 | GROMACS simulation | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.4.1 |
| 14 | GROMACS simulation | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.4.1 |
Version History
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Views: 1222 Downloads: 164 Runs: 0
Created: 2nd Jun 2025 at 11:04
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