Hi,I am a brand new user in using Rosetta.
In my case, I want to dock a ligand to a protein with the protein conformation fixed.
I have tried default protocol of ligand_docking but it did not work.
The conformation of some side chains changed.
So, does someone have the idea of designing a proper protocol to achieve this goal?
Thanks in advance.
My purpose is verifying the mechanism of docking an oligosaccharide molecule to a hexosaminidase.
Actually this mechanism has already been confirmed by the complex structures solved by X-ray crystallography.
In this mechanism, the side chain conformations of some critical interface residues should not be changed.
However, in the docking results, the conformations of these residues changed.
So, I hope that there is a protocol through which the ligand can be docked to the protein with the conformation of side chain fixed.
In this way, I think that the docking score may make more sense.