Rosetta Ligand Docking Error: Pose Has No Jumps

'Rosetta Ligand Docking Error: Pose Has No Jumps'

The error message "ERROR: Pose has no jumps!" indicates that the input PDB file used for ligand docking does not contain any defined connections (jumps) between different parts of the structure. This is a critical requirement for ligand docking as it involves placing the ligand within a specific binding site defined by the connections within the protein structure.

Possible Causes and Solutions:

• Incorrect Input PDB File: Verify that the input PDB file is correctly formatted and contains the necessary information about the protein structure, including connections between different parts of the protein. Double-check that the PDB file represents the intended protein structure and that the receptor and ligand are properly defined.
• Missing or Incorrect Jumps: The PDB file might be missing jump information, or the defined jumps might be incorrect. Review the PDB file manually to confirm the presence and accuracy of jump information. Use tools like PyMOL or other structure visualization software to inspect the structure and verify jump definitions.
• Incorrect Parameters: Check the parameters used in the ligand docking protocol. Ensure that the parameters are appropriate for the specific docking task and that they are correctly set. Refer to the Rosetta documentation for detailed information about the ligand docking protocol parameters.

Troubleshooting Steps:

1. Inspect the PDB File: Carefully examine the input PDB file to identify any potential issues with the structure definition or jump information. If the PDB file does not contain explicit jump information, try defining them manually by adding appropriate LINK records.
2. Adjust Input Parameters: Try using different parameters in the ligand docking protocol. Experiment with parameters like the search space size, scoring function, and docking algorithm to see if any combination resolves the error.
3. Use Different Input File Formats: Rosetta accepts various input file formats. Consider using a different file format like Atom Tree Diff (ATD) format for inputting the structure. Consult Rosetta documentation for instructions on how to generate and use ATD files.
4. Consult Rosetta Documentation and Support: Review the Rosetta documentation thoroughly for detailed information about ligand docking protocols and troubleshooting. If the issue persists, seek assistance from the Rosetta community forum or the official Rosetta support channel for further guidance.

Remember: The "Pose has no jumps!" error highlights the importance of accurate structure representation and jump information for successful ligand docking in Rosetta. By carefully inspecting the input file and parameters, you can likely identify and address the source of the error.