Thanks for the super detailed reply, Bipin. I will try this out!
On Fri, Jan 31, 2014 at 3:04 PM, bipin singh bipinel...@gmail.com wrote:
Inter helical angle using *g_bundle *
# 1. Do in make_ndx:
# make_ndxGenerate indexes describing extremities of
# the two helices. Select the CA of residues belonging
#the extremities of each helix.
make_ndx -f NAME.gro -o NAME_CROSSANGLE.ndx
# Define other groups you need
# Define 4 groups corresponding to the ends of the two helices
# ...
# q
# 2. Do in a text editor:
# Merge the 4 index groups, corresponding to helices ends, in order to get
# two index groups, each containing either the beginning of the two
# helices or the ends of the two helices. See g_bundle's online help.
# The number of residues selected for each helix has to be the same.
# 3. Do in g_bundle:
# g_bundleGet coordinate of vectors describing the helices
echo 0 1 | g_bundle -f NAME.xtc -s NAME.tpr -n NAME_CROSSANGLE.ndx \
-dt XX -b -e -na 2 -oa NAME_CROSSANGLE.pdb\
g_bundle.CROSSANGLE.out
# -na 2; there are two axes this time
# -oa NAME_CROSSANGLE.pdb ; to get the coordinates of the axes and
check the angles given by the software
# rm, Remove some unuseful files genererated by g_bundle:
rm bun_len.xvg bun_dist.xvg bun_z.xvg bun_tilt.vxg bun_tiltl.xvg
bun_tiltr.xvg
# The first time, it might be helpful to open NAME_CROSSANGLE.pdb in rasmol
or
# vmd to visualize the data you are handling and check wether you define
your
# index correctly... and also two understand the structures of the data you
# are handling.
# The next part is dirty and could be automated with a smart script:
# 4. Do in g_ traj
# g_traj transform the .pdb trajectory in a file format easier to handle,
# i.e a .xvg file.
echo 0 | g_traj -f NAME_CROSSANGLE.pdb -s NAME_CROSSANGLE.pdb \
-ox NAME_CROSSANGLE.xvg g_traj.CROSSANGLE.out
#In the header of the .xvg file, you have this:
# @ legend string 0 atom 1 X
# @ legend string 1 atom 1 Y
# @ legend string 2 atom 1 Z
# @ legend string 3 atom 2 X
# @ legend string 4 atom 2 Y
# @ legend string 5 atom 2 Z
# @ legend string 6 atom 3 X
# @ legend string 7 atom 3 Y
# @ legend string 8 atom 3 Z
# @ legend string 9 atom 4 X
# @ legend string 10 atom 4 Y
# @ legend string 11 atom 4 Z
# @ legend string 12 atom 5 X
# @ legend string 13 atom 5 Y
# @ legend string 14 atom 5 Z
# @ legend string 15 atom 6 X
# @ legend string 16 atom 6 Y
# @ legend string 17 atom 6 Z
# 01.35431.23062.11210.85610.8589...
# 201.40021.06922.04280.89430.7557...
# 401.3591.07932.13410.86860.7528...
# ......
# 5. Do in Microsoft Excel or equivalent
# Import the .xvg file. You'll get a 19-column file. The first column
# correspond to the time. The next 9 columns are (x,y,z) coordinates of 3
# points belonging to the vector describing the first helix and the next 9
# are coordinate of 3 points belonging to the second helix.
# When this point is reached, you can define the vectors describing the
# helices (by substracting coordinate of atom 3 and 1 and atom 6 and 4),
# normalize them (by dividing the vector by their norm) and calulate their
# dot-product in excel.
# The dot product of two normalized vectors is the cosine of their
# cross-angle.
Disclaimer: Copied from an old gromacs discussion.
On Thu, Jan 30, 2014 at 2:06 PM, rajat desikan rajatdesi...@gmail.com
wrote:
Hi All,
Any suggestions?
Thanks.
On Mon, Jan 27, 2014 at 5:01 PM, rajat desikan rajatdesi...@gmail.com
wrote:
Hi All,
I am trying to calculate the angle between the axes of two alpha
helices
(say A and B) in my simulation. I have separate index files for the
residues pertaining to each helix.
I calculated the tilt.xvg for both A and B. The output is slightly
confusing. tilt_A.xvg when viewed with xmgrace -nxy shows 27 data sets.
What do these correspond to? (Helix A has 34 residues). Similarly for
bending_A.xvg
How do I go about this? Is this the right way to calculate the relative
helix axis angle?
Thanks,
--
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
--
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
--
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