My Prime refinement job died with an error referring to an xxxz residue, where xxx is a 3-letter residue name. What does this mean?
This message means that you have an isolated residue in your structure. For Prime to run, you must either delete this residue or change its residue name (using the Build panel) to UNK, LIG, or some other 3-letter name that is not one of the standard or modified amino acid residue names. • I successfully built a homology model with Prime, but my ligand does not have the correct bond orders. I want to use this structure as input for another Prime job (e.g., a loop prediction). What should I do? It’s very likely that you will not need to do anything. Before the main Prime job is run, a program is automatically run that will fix the bond orders and formal charges of the ligand, as long as the hydrogens in the structure are correctly placed.
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