Thanks a lot XAvier! On Sat, Jun 5, 2010 at 2:10 PM, XAvier Periole <x.peri...@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 < > 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 >> > > -- > > 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 > > > > -- > 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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