[gmx-users] Helix Tilt Calculation

[Anirban Ghosh]

Thanks XAvier and George for the reply. Yes the N and C terminus are on the
opposite sides of the bilayer. So I can take the values of the even TMs as
(180 - respective value), correct?

Regards,

Anirban

On Fri, Jun 4, 2010 at 8:00 PM, George Khelashvili
<gek2009 at med.cornell.edu>wrote:

> Hi,
>
> 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.
>
> George
>
>
> 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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