[gmx-users] Helix Tilt Calculation

XAvier Periole x.periole at rug.nl
Fri Jun 4 16:46:24 CEST 2010

On Jun 4, 2010, at 4:26 PM, 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.
Could that be a result of the N et  C terminus being not on the same  
of the membrane bilayer ?
> Regards,
> Anirban
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