[gmx-users] g_bundle!

[priyanka srivastava]

thanku so so much for the help. I guess I have done it
in the right way now because the results seem to be
meaningful this time.

One thing more, since I am calculating the angle
between helical axis and z axis, and specify -z with
g_bundle, so I have taken -na=1.

I hope this is alright.

Another thing is, Is there any way to find out the
center of the system and then translating the system
(alongwith the box) to 0,0,0. I tried using -center
with trjconv but it shows a shift of all the atoms
outside the box. I guess although it does move the
system at 0,0,0 but the box remains at its original
position. 

Pri...


--- TJ Piggot <t.piggot at bristol.ac.uk> wrote:

> use the program make_ndx or just edit the .ndx file
> using a text editor
> 
> Tom
> 
> --On 21 June 2007 11:03 -0700 priyanka srivastava
> <priyankaps4 at yahoo.com> 
> wrote:
> 
> > Does this mean defining my own .ndx file and not
> using
> > the default one?
> >
> > If yes, can you please drop some hints of how to
> make
> > the .ndx file for this purpose.
> >
> > thanks and regards,
> > Pri...
> >
> >
> > --- Alan Dodd <anoddlad at yahoo.com> wrote:
> >
> >> I've used g_bundle a lot for just this sort of
> >> thing.  You need to define the top and bottom of
> the
> >> helix as seperate groups, and define them *very*
> >> carefully - it does make a difference how you do
> it,
> >> presumably because g_bundle just plots the axis
> >> between the COM of both groups?  I usually define
> as
> >> close to 1 complete turn of the backbone of the
> >> helix at each end as possible.
> >> Your output is not surprising, given what you've
> >> asked the program for - the axis between two
> points
> >> that precisely overlap ;-)
> >>
> >> ----- Original Message ----
> >> From: priyanka srivastava <priyankaps4 at yahoo.com>
> >> To: gmx-users at gromacs.org
> >> Sent: Wednesday, June 20, 2007 3:27:42 PM
> >> Subject: [gmx-users] g_bundle!
> >>
> >>
> >> Dear All,
> >>
> >> I want to calculate tilt angle of a peptide
> inserted
> >> inside the lipid bilayer (i.e. angle between the
> >> helical axis and bilayer normal). From previous
> >> posts
> >> I got an idea that g_bundle wud solve my problem.
> >>
> >> I am issuing the following on the command line:
> >>
> >> g_bundle -f test.xtc -s test.tpr -na 2 -z -tu ps
> >>
> >> This asks me to "Select a group of top and a
> group
> >> of
> >> bottom atoms"
> >>
> >> Group     0 (      System) has 12877 elements
> >> Group     1 (     Protein) has   102 elements
> >> Group     2 (   Protein-H) has    79 elements
> >> Group     3 (     C-alpha) has    10 elements
> >> Group     4 (    Backbone) has    31 elements
> >> Group     5 (   MainChain) has    41 elements
> >> Group     6 (MainChain+Cb) has    49 elements
> >> Group     7 ( MainChain+H) has    54 elements
> >> Group     8 (   SideChain) has    48 elements
> >> Group     9 ( SideChain-H) has    38 elements
> >> Group    10 ( Prot-Masses) has   102 elements
> >>
> >> when I chose "1" and "1" it gives all angles as
> 90,
> >> which is wrong and bun_tiltr is reported as
> "nan".
> >> The
> >> manual says that "the program reads two index
> groups
> >> and divides both of them in -na parts".
> >> I am a lil confused! what should be my choice
> here?
> >>
> >> regards,
> >> Pri...
> >>
> >>
> >>
> >>
> >>
> >>
> >
>
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> 
> 
> ----------------------
> TJ Piggot
> t.piggot at bristol.ac.uk
> University of Bristol, UK.
> 
> _______________________________________________
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