I am using kic loop protocol to refine a big loop with 12 aa with rosetta. I noticed that the energy is positive from generated .PDB file:
Shouldn't it be a negative value in principle?
BTW, how can we tell Rosetta treat SS bridge in the latest version? I would suggest why not add an option to Rosetta so that it can treat SS bond automatically according to SS atoms distance. Many software such as: Modeller, Gromacs, Amber can do this automatically. It shouldn't be so difficult to achieve this function.
thx a lot