I run the ligand docking protocol to dock a small chemical to protein.
this is my flag
-dock_pert 30 5
-start_from 1.36 50.07 23.4
When I take a look on the output files, I saw the lowest score out files of this run is far away together (up to 25 Angstrom). Is it normal? If it is normal, Can I say the chamical was moved around my protein?
As I expected the output will local in the sphere with dimeter about 10Anstrong.
This is more or less the same question as https://www.rosettacommons.org/node/9459 right? Or is there some subtle aspect I’m missing? (I’ll admit I don’t understand what you mean by “far away together”.)