[gmx-users] Helix Tilt Calculation

George Khelashvili gek2009 at med.cornell.edu
Fri Jun 4 16:30:08 CEST 2010


Your 150 degree angle is in reality 30 degrees (180-30). This is a 
matter of defining the vector representing your helix vs. the direction 
of the z axis. If your vector points in the opposite direction of the z 
axis, then your angle will be between 90 and 180 degrees.


Anirban Ghosh wrote:
> Hi ALL,
> I am using g_angle to calculate the tilt of individual helix in a 
> rhodopsin GPCR with respect to z axis. In the index file I am defining 
> the top and bottom of each helix with first 4 and last 4 residues of 
> that helix respectively. Strangely, I am getting the tilt angle of the 
> odd helices like TM1, 3 and 5 in the range of 30 degrees, but the even 
> helices TM2, 4 and 6 are giving value in the range of 150 degrees. But 
> visual inspection of the simulation does not show such huge deviation. 
> Why is it giving so? Am I doing anything wrong here? Any suggestion is 
> welcome. Thanks a lot in advance.
> Regards,
> Anirban

George Khelashvili, Ph.D.
Department of Physiology and Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Room LC501
New York, NY, 10065, USA
gek2009 at med.cornell.edu
Phone: 1-212-746-6539
Fax:   1-212-746-6226

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