[gmx-users] Helix Tilt Calculation

[Anirban Ghosh]

Thanks a lot XAvier!

On Sat, Jun 5, 2010 at 2:10 PM, XAvier Periole <x.periole at rug.nl> wrote:

>
> Yes,
> or inverse your sections from the index!
>
>   On Jun 5, 2010, at 10:10 AM, Anirban Ghosh wrote:
>
>   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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