Hi, I am having trouble minimizing a protein that contains trehalose. Unfortunately, Rosetta does not like trehalose and always deforms it.
I have no problems with glucose, that's weird because trehalose is a glucose disaccharide. I am using the flag -include_sugars and the relaxed structure has unrealistic energies because it forces the formation of non-existing bonds. The main problem is that rosetta assumes it is ->2)-alpha-D-GlucP