[gmx-users] g_bundle issue
Hi ALL, I tried to calculate the helix tilt of a single helix (TM5) among 7 helices using g_bundle. In the index file I defined the two groups (top bottom) as the C-alpha of the first 5 and last 5 residues of TM5 respectively. But in the bun_tilt.xvg file I am getting the values as: --- # This file was created Thu May 20 15:29:50 2010 # by the following command: # g_bundle -f prot.xtc -s prot.tpr -n TM5_top_bot.ndx -na 1 # # g_bundle is part of G R O M A C S: # # GRowing Old MAkes el Chrono Sweat # @title Axis tilts @xaxis label Time (ps) @yaxis label (degrees) @TYPE xy 0 0 2 0.0197823 4 0 6 0.0197823 8 0 10 0 12 0.0197823 14 0 16 0.0197823 18 0 20 0.0279765 22 0 24 0 26 0.0197823 28 0 30 0 32 0 34 0 36 0 38 0.0197823 And when plotted it gives a blank plot. Why it is coming like this? Am I doing anything wrong? Any suggestion is welcome. The contents of the index file is: [ top ] 1844 1850 1858 1866 1878 1896 1904 1913 1922 1940 1948 1956 1965 1974 1983 1991 [ bottom ] 2000 2008 2014 2024 2032 2041 2050 2067 2079 2092 2101 2109 2118 2124 2132 2138 2146 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
Re: [gmx-users] g_bundle issue
Have you tried using the -z option to calculate the angle with respect to to the z axis? I vaguely remember having an issue like this a few years ago and this fixed the problem, sorry I can't be more specific. Cheers Tom Anirban Ghosh wrote: Hi ALL, I tried to calculate the helix tilt of a single helix (TM5) among 7 helices using g_bundle. In the index file I defined the two groups (top bottom) as the C-alpha of the first 5 and last 5 residues of TM5 respectively. But in the bun_tilt.xvg file I am getting the values as: --- # This file was created Thu May 20 15:29:50 2010 # by the following command: # g_bundle -f prot.xtc -s prot.tpr -n TM5_top_bot.ndx -na 1 # # g_bundle is part of G R O M A C S: # # GRowing Old MAkes el Chrono Sweat # @title Axis tilts @xaxis label Time (ps) @yaxis label (degrees) @TYPE xy 0 0 2 0.0197823 4 0 6 0.0197823 8 0 10 0 12 0.0197823 14 0 16 0.0197823 18 0 20 0.0279765 22 0 24 0 26 0.0197823 28 0 30 0 32 0 34 0 36 0 38 0.0197823 And when plotted it gives a blank plot. Why it is coming like this? Am I doing anything wrong? Any suggestion is welcome. The contents of the index file is: [ top ] 1844 1850 1858 1866 1878 1896 1904 1913 1922 1940 1948 1956 1965 1974 1983 1991 [ bottom ] 2000 2008 2014 2024 2032 2041 2050 2067 2079 2092 2101 2109 2118 2124 2132 2138 2146 Regards, Anirban -- Dr Thomas Piggot University of Southampton, UK. -- 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] g_bundle issue
Hi ALL, I tried to calculate the helix tilt of a single helix (TM5) among 7 helices using g_bundle. In the index file I defined the two groups (top bottom) as the C-alpha of the first 5 and last 5 residues of TM5 respectively. But in the bun_tilt.xvg file I am getting the values as: --- # This file was created Thu May 20 15:29:50 2010 # by the following command: # g_bundle -f prot.xtc -s prot.tpr -n TM5_top_bot.ndx -na 1 # # g_bundle is part of G R O M A C S: # # GRowing Old MAkes el Chrono Sweat # @title Axis tilts @xaxis label Time (ps) @yaxis label (degrees) @TYPE xy 0 0 2 0.0197823 4 0 6 0.0197823 8 0 10 0 12 0.0197823 14 0 16 0.0197823 18 0 20 0.0279765 22 0 24 0 26 0.0197823 28 0 30 0 32 0 34 0 36 0 38 0.0197823 And when plotted it gives a blank plot. Why it is coming like this? Am I doing anything wrong? Any suggestion is welcome. The contents of the index file is: [ top ] 1844 1850 1858 1866 1878 1896 1904 1913 1922 1940 1948 1956 1965 1974 1983 1991 [ bottom ] 2000 2008 2014 2024 2032 2041 2050 2067 2079 2092 2101 2109 2118 2124 2132 2138 2146 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] g_bundle issue
Hi ALL, I tried to calculate the helix tilt of a single helix (TM5) among 7 helices using g_bundle. In the index file I defined the two groups (top bottom) as the C-alpha of the first 5 and last 5 residues of TM5 respectively. But in the bun_tilt.xvg file I am getting the values as: --- # This file was created Thu May 20 15:29:50 2010 # by the following command: # g_bundle -f prot.xtc -s prot.tpr -n TM5_top_bot.ndx -na 1 # # g_bundle is part of G R O M A C S: # # GRowing Old MAkes el Chrono Sweat # @title Axis tilts @xaxis label Time (ps) @yaxis label (degrees) @TYPE xy 0 0 2 0.0197823 4 0 6 0.0197823 8 0 10 0 12 0.0197823 14 0 16 0.0197823 18 0 20 0.0279765 22 0 24 0 26 0.0197823 28 0 30 0 32 0 34 0 36 0 38 0.0197823 And when plotted it gives a blank plot. Why it is coming like this? Am I doing anything wrong? Any suggestion is welcome. The contents of the index file is: [ top ] 1844 1850 1858 1866 1878 1896 1904 1913 1922 1940 1948 1956 1965 1974 1983 1991 [ bottom ] 2000 2008 2014 2024 2032 2041 2050 2067 2079 2092 2101 2109 2118 2124 2132 2138 2146 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
