I am using de novo evolution, I have a ligand and protein complex, I drag the ligand out of the complex in hierarchy window, and I set the protein as an input receptor, and the ligand as an input ligand scaffold, using ludi fragment libraries.
I can start the job, but the job finish in seconds with 0 ligands result, it seems the program does not use the library yet.
I try to move ligand to another 3d window, useless, the result is same.