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.