The RosettaCM requires Ligands must be added to all templates with a non-zero weight in the XML file!
In my case, the templates represent different parts of the target, so some template includes the ligand while some template does not. Do I really need to add the ligand to the template that does not have the ligand?
If it is necessary, how to do it? It is not likely to use some alignment to "estimate" the ligand location in the template.