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.
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