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 <gek2...@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 > gek2...@med.cornell.edu > Phone: 1-212-746-6539 > Fax: 1-212-746-6226 > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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