[gmx-users] g_helixorient help

Fri Jan 31 10:34:21 CET 2014

Inter helical angle using *g_bundle *
# 1. Do in make_ndx:
# make_ndx    Generate 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_bundle    Get coordinate of vectors describing the helices
echo 0 1 | g_bundle -f NAME.xtc -s NAME.tpr -n NAME_CROSSANGLE.ndx \
                    -dt XX -b YYYY -e ZZZZ -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"
#  0    1.3543    1.2306    2.1121    0.8561    0.8589    ...
#  20    1.4002    1.0692    2.0428    0.8943    0.7557    ...
#  40    1.359    1.0793    2.1341    0.8686    0.7528    ...
#  ...    ...

# 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 <rajatdesikan at gmail.com>wrote:

> Hi All,
> Any suggestions?
>
> Thanks.
>
>
> On Mon, Jan 27, 2014 at 5:01 PM, rajat desikan <rajatdesikan at 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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-- 

*--------------------Thanks and Regards,Bipin Singh*