MD protein-ligand workflow (from PDB structure)

computational-chemistry-htmd-analysis/main-workflow

Author(s)

version Version
2
last_modification Last updated
Jul 21, 2020
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
cheminformatics
moleculardynamics
computational-chemistry

Features

Tutorial
hands_on High Throughput Molecular Dynamics and Analysis
workflow Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00034
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
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

Input Label
Input parameter PDB code (e.g. 6hhr)
Input parameter Ligand name (e.g. AG5E)

Outputs

From Output Label
Input parameter PDB code (e.g. 6hhr)
Input parameter Ligand name (e.g. AG5E)

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/get_pdb/get_pdb/0.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/2.4.2.2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_acpype/ambertools_acpype/19.11 View in ToolShed
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2019.1.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2019.1.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_merge_topology_files/gmx_merge_topology_files/3.2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2019.1.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.4.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2019.1.4 View in ToolShed

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

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
2 2a74c6770 2020-07-21 11:11:57 fix workflows
1 3e9586df2 2020-05-20 17:27:02 HTMD tutorial (#1837)

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