What do I do if Prime Covalent Docking job fails with the following error:

ERROR: Failure in rotatable bond assignment, could not determine relationship between atoms...

This error typically points to problems with the PDB atom naming of the ligand atoms. Please try the following:

1. Place the ligand in the Workspace.
2. Choose Edit → Build → Atom Properties.
3. Select 'PDB Atom Name' from the Properties option menu
4. In the 'Set unique PDB atom names within residues' section, click the 'All' button

This assigns a unique PDB atom name for each of the ligand atoms, which should allow the job to run.

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