Galaxy | Tool Preview

OpenDUck chunk (version 0.1.1)
Cutoff for chunk generation (in angstroms)
Parameters for the protein-ligand interactions
Parameters for the protein-ligand interaction 0
Return a tar file containing all files produced during the simulations.

What it does

Produce chunk automatically for dynamic undocking (DUck). Chunking entails selecting a region of the protein which is used for a DUck simulation.

This Galaxy tool uses OpenDUck, an open-source implementation of the original DUck method, using OpenMM and AmberTools.


Input

  • PDB file for protein
  • SDF/MOL file for ligand
  • Parameters defining the protein-ligand interaction

Output

  • PDB file containing the chunked protein ready for system preparation.

A tar file is also produced as a optional output, containing all files produced by the tool.