Re: [gmx-users] Helix Tilt Calculation
Thanks a lot XAvier! On Sat, Jun 5, 2010 at 2:10 PM, XAvier Periole 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 listgmx-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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Helix Tilt Calculation
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 > 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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Helix Tilt Calculation
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 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 listgmx-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 listgmx-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
Re: [gmx-users] Helix Tilt Calculation
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 listgmx-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
Re: [gmx-users] Helix Tilt Calculation
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 -- gmx-users mailing listgmx-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 listgmx-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
