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
side
of the membrane bilayer ?
Regards,
Anirban
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