C-docker

Dear All,

I am facing problem with C-Docker docking studies. I am getting negative values in C-docker energy. I understand it can be due to ligand strain energy. But how to reduce this ligand strain energy . Then the second problem is docking a smaller  molecule in bigger sphere. This problem as solved with site partition in the ligandFit. What about in C-docker?

Pl suggest.

Thanks & Regards’

Awantika Shrivastava