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the output of ligand docking

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the output of ligand docking

Dear all,
I run the ligand docking protocol to dock a small chemical to protein.
this is my flag
-dock_pert 30 5
-improve_orientation 1000
-harmonic_torsions 10
-harmonic_Calphas 0.3
-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

Post Situation: 
Fri, 2015-07-03 01:27

This is more or less the same question as right? Or is there some subtle aspect I'm missing? (I'll admit I don't understand what you mean by "far away together".)

Fri, 2015-07-03 13:14