MD protein-ligand workflow (from PDB structure)

Run Workflow in Galaxy

• Galaxy Main
• Galaxy Australia
• Galaxy France
• Galaxy Europe
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Parameter\nPDB code e.g. 6hhr"];
  style 0 fill:#ded,stroke:#393,stroke-width:4px;
  1["ℹ️ Input Parameter\nLigand name e.g. AG5E"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["Get PDB file"];
  0 -->|output| 2;
  3["Search in textfiles"];
  2 -->|output| 3;
  4["Search in textfiles"];
  2 -->|output| 4;
  1 -->|output| 4;
  5["GROMACS initial setup"];
  3 -->|output| 5;
  6["Compound conversion"];
  4 -->|output| 6;
  7["Generate MD topologies for small molecules"];
  6 -->|outfile| 7;
  8["Merge GROMACS topologies"];
  7 -->|gro_output| 8;
  5 -->|output1| 8;
  5 -->|output2| 8;
  7 -->|output| 8;
  9["GROMACS structure configuration"];
  8 -->|complex_gro| 9;
  10["GROMACS solvation and adding ions"];
  8 -->|complex_top| 10;
  9 -->|output| 10;
  11["GROMACS energy minimization"];
  10 -->|output2| 11;
  10 -->|output1| 11;
  12["GROMACS simulation"];
  5 -->|output3| 12;
  10 -->|output2| 12;
  11 -->|output1| 12;
  13["GROMACS simulation"];
  5 -->|output3| 13;
  10 -->|output2| 13;
  12 -->|output1| 13;
  12 -->|output5| 13;
  14["GROMACS simulation"];
  10 -->|output2| 14;
  13 -->|output1| 14;
  13 -->|output5| 14;

Inputs

Outputs

Tools

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Hands-on: Importing a workflow

• Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
• Click on galaxy-upload Import at the top-right of the screen
• Provide your workflow
  • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
  • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
• Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/htmd-analysis/workflows/main_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows