[gmx-users] Helix Tilt Calculation

[XAvier Periole]

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
>
>
>
> -- 
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> -- 
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100605/3d63ef4f/attachment.html>