Workflow Type: Galaxy
Open
High Throughput Molecular Dynamics and Analysis
Associated Tutorial
This workflows is part of the tutorial MD protein-ligand workflow (from PDB structure), available in the GTN
Thanks to...
Tutorial Author(s): Simon Bray, Tharindu Senapathi, Christopher Barnett, Björn Grüning
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
2.0 (earliest) Created 25th Jun 2024 at 11:02 by Helena Rasche
Added/updated 4 files
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Views: 138 Downloads: 47
Created: 25th Jun 2024 at 11:01
Last updated: 25th Jun 2024 at 11:02
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