[gmx-users] Helix Tilt Calculation

Anirban Ghosh reach.anirban.ghosh at gmail.com
Fri Jun 4 16:26:53 CEST 2010


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


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100604/c9ff3edb/attachment.html>

More information about the gromacs.org_gmx-users mailing list