I am trying to use enzyme design app in Rosetta 3.4 with a small ligand docked into an enzyme (no enzyme-ligand covalent connection), and I have two questions about it.
The first is, I do not know which residues of the protein take part in the catalysis, so I cannot form a .cst file. Would results of such an enzyme design job without a .cst file be somewhat reliable or total rubbish? What else could you suggest me to do about it, is there any way to compensate the absence of such catalytic knowledge, or is the program only designed to work with appropriate catalytic constraints?
My second question is, at the moment, I made enzyme design application work. There is no .cst file as input, only the flags, unbound pdb, and enzyme docked ligand pdb. The resulting job finishes gracefully and gives some final structures, all being identical (also with identical scores). Why could this be happening? The flag file I used is what is suggested by the demos, with only minor changes.
I would be glad if you could help me with these,