[gmx-users] g_helixorient help

Fri Feb 7 17:47:24 CET 2014

Thanks for the super detailed reply, Bipin. I will try this out!

On Fri, Jan 31, 2014 at 3:04 PM, bipin singh <bipinelmat at gmail.com> wrote:

> 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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
>
>
>
> *--------------------Thanks and Regards,Bipin Singh*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore