Now, I am studying about protein design in carbohydrate modifying enzyme. I am very new for Rosetta and trying to use Rosetta Design to change the product specification. I have constructed intermediate molecules in catalytic step and docked into the active site of the enzyme by another program. Then I performed protein design by using fixbb and enzyme_design (without constraint) applications to redesign residues in the binding site around intermediate molecules. But they seem like they could not see intermediate molecules. Both fixbb and enzyme_design applications changed the residues in the binding site to interact with themselves instead. Here is an input files, does it has any option or command that I miss to make an interaction or any program would fit to my purpose?
Any advice would be much appreciated