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PostPosted: Wed Aug 26, 2009 4:26 pm 
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Hello everybody,

I want to dock a sort of oriented helical ligand on a protein. More precisely, I want to test some particular orientations of this ligand. The idea is to rotate the ligand by n degrees about its long principal axis and do a local optimization or a simulated annealing. I have read the manual for 4.2 which tells me that I'm suppose to use quat0. However, the dpf file created by ADT do not specify quat0 , but axisangle0. Should I use:

axisangle0 x y z n

with x y z being the vector of the principal axis and n the number of degrees? Axisangle0 does not appear in the Autodock documentation.

Regards,
Nicolas

ps: hope I'm not redundant with the Autodock mailing list


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PostPosted: Wed Aug 26, 2009 9:08 pm 
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The source code suggests that quat0 and axisangle0 are treated as equivalent in AD4+. quaternion0 seems to be reserved for specifying old style quaternions.


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PostPosted: Thu Aug 27, 2009 10:26 am 
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I browsed the autodock logs and found this line:
Code:
Initial axis-angle,  (nx,ny,nz,ang) =   ( -0.340, -0.940, 0.000, 90.0 deg ),
Initial quaternion,  (x,y,z,w) =        ( -0.240, -0.665, 0.000, 0.707 ),


Apparently, the parameters of axisangle0 are the 3D coordinates of the rotation axis + the angle. They seem to correspond to the quaternion calculated by Autodock since cos(90/2) = 0.707. Anyway, setting axisangle0 doesn't seem bias the ligand orientation with simulated annealing. The final orientations are far beyond want I want. I guess it only works with local search.


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