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 ?
If you’re using the ligand_docking application, then the ligand (particularly the nbr_atom) should *start* at the position provided by the -start_from option. During docking, there’s a possibility that the ligand will move substantially from that position, particularly if it’s a bad one. (The ligand “shoots out” of the pocket due to clashes, for example.)
Are you consistently getting the ligand to be 50+ Ang away from where you want it to be, or is this movement just one structure? (Ligand docking runs are stochastic, and you will occasionally get ligands which fly out of the pocket. Those should be easy to discard based on their poor energies, though.)
Also, is there anything particular about the location where the ligand does end up? Is it in contact with another part of the protein? Is it similar to the input coordinates for the ligand? If so, that might indicate that the -start_from option isn’t being correctly recognized. (What is your full commandline and options file?)