Dear all,
I run the ligand docking protocol to dock a small chemical to protein.
this is my flag
-packing
-no_optH
-ex1
-ex1aro
-ex2
-docking
-dock_pert 30 5
-ligand
-improve_orientation 1000
-minimize_ligand
-harmonic_torsions 10
-minimize_backbone
-harmonic_Calphas 0.3
-soft_rep
-old_estat
-start_from 1.36 50.07 23.4
-protocol abbrev2
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.
Could some one help me?
Thank in advance and best regards
Phan Vy
Category:
Post Situation:
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".)