I run ligand docking protocol to dock a small chemical on my protein.
I set up the inital position of ligand is "-start_from 1.36 50.07 23.4".
Follow the document, the nbr_atom of the ligand is chosen near the inital position of ligand. But when I check the log file, I saw the nbr_atom of the ligand is far away from the inital position of ligand: 44.03500058226830 112.4592971897935 22.25074880071337
4.886590717968414 0.06526207982382815 17.92231676318689
Can some one help me understand about this ?
Thank a lot