ADL: ligand center and tran0

Nicolas Sapay nicolas.sapay at cermav.cnrs.fr
Wed Mar 17 03:29:30 PDT 2010



Olivier Danot a écrit :
> Thanks Nicolas,
> So, the tran0 coordinates should be those of the geometrical center of 
> the ligand in the frame of reference, right ?
If you consider the grid coordinates as your frame of reference, yes.
> But when I calculate the average of the x (for instance) coordinates 
> of the atoms of the ligand (which should be the x coordinate of the 
> geometrical center), it is slightly different form the x coordinate of 
> tran0.
> In fact, my problem is: can the coordinates of the geometrical center 
> of the poses of the ligand be extracted easily from the dlg files or 
> do I have to calculate the average coordinates myself ? I  suspect 
> that they are somewhere in the file because they are needed for the 
> representation of the ligand as spheres.
I'm not sure to following you. "tran0" is the coordinates to which the 
ligand will translated at the begining of the docking simulation. For 
example, if your grid is centred on (0,-6, 3) and you chose to start the 
docking from this position, tran0 will be (0,6,3). During the 
simulation, the docking algorithm will modify the position of the ligand 
centre to improve the docking score. At the end, the centre of the 
ligand will be (most probably) different that "tran0", or "about", 
except if you shutdown translations in the Autodock input file. IIRC, 
the final docked state should indicate the initial and final position of 
the ligand centre. Browse the dlg and look for the keyword "FINAL DOCKED 
STATE". The lines below should contain all the information you are 
looking for. Otherwise, one of the Python scripts included in the 
AutodockTools may help you (on Linux, they are located in 
/path/to/mgltools/MGLToolsPckgs/AutoDockTools/Utilities24).

Nicolas
> Thanks
> Olivier
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