DOCK Blaster:Failure with PDB code

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Unfortunately, we were unable to run your DOCK Blaster job starting from a PDB code alone.


This message indicates that we could not automatically find a ligand to use to identify the binding site, and to use as a control for automated docking.

In the future, we may use automatic binding site identification software in this case. For now, if you know where the binding site on this protein is,l you may be able to rescue this case. Please use the "start with a structure" entry point into DOCK Blaster.

  • Step 1. Download the PDB file.
  • Step 2. Identify the binding site. Pick 3 residues that triangulate the binding site. They do not have to be involved in the catalytic process, but the center of mass of these three residues should be where you want the ligand to go.
  • Step 3. Scrape/copy these three residues into a file. Call the file "bindingsite.pdb". Now start DOCK Blaster using files.
  • Step 4. If problems persist, please write us, quoting the final DOCK Blaster job ID number.

Other problems

In addition to "no atoms found", there may be more than one ligand. In this case, we should give you a choice. For now, the approach is to enter the three letter code of the ligand you want to use in the Parser, in addition to the PDB code.

Good luck!