ADL: ligand center and tran0

Nicolas Sapay nicolas.sapay at cermav.cnrs.fr
Wed Mar 17 01:32:45 PDT 2010


Hi Olivier,

"about" is the geometrical center about which the ligand will be 
rotated. This is the *geometrical* centre of the ligand, not the centre 
of mass. Its coordinates correspond to the frame of reference *of the 
ligand*. Usually, I centre my ligand on the origin, which means 
"about"=0,0,0.

"tran0" is the initial position of the ligand in the frame of reference 
*of the protein* (of the grid actually), which is not necessarily the 
same that the one of the ligand. So, tran0 is not necessarily equal to 
"about"

Cheers,
Nicolas

Olivier Danot a écrit :
> Hi everybody,
> It seems that the tran0 parameter (or maybe tran0+about) in the dlg 
> file defines the center of the ligand for each pose. However, in a 
> series of rigid dockings I have done with Autodock4, neither tran0 nor 
> tran0+about correspond to the average of the coordinates of the ligand 
> (there is a 0.1-1 Angström difference in the coordinates). Is there 
> something I misunderstood ?
> Thanks
> Olivier
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