Structure prediction

I set up a homology model with the setup_RosettaCM.py
It creates a set of threaded models, an xml file with commands, and a flags command that points to the input file and the xml. When I run the rosetta_scripts command with this flags and xml, I get a segmentation fault. I find the error messages difficult to understand. 

Here is the command, screen output, flags, xml, and CRASH.log

The FAQ of robetta said "You can load multiple templates, modify the alignments, add constraints, and more before submitting.“ However, I cannot find the option for loading multiple templates on the Robetta webserver. Is that possible?

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.

Hello Everyone,

I am trying to mutate multiple residues of a peptide with NCAA to determine their structure and ΔΔG of mutation on Rosetta. 

I would be grateful if anyone could share any research article, material or guidance to proceed on this matter.

P.S. - I am a beginner at Rosetta without any bacl ground in coding or bioinformatics. Any help and advice is appreciated.