[gmx-users] query on using g_bundle

[Dilraj Lama]

hello gmx-users,
                I have some queries regarding the usage of g_bundle.

1) First is regarding defining the groups in the index file.
       I defined the groups as C-alpha_&_r_99-116,C-alpha_&_r_120-137.But I found in some post
that definition of index groups should have CA atoms of the first and last residues of the
helix residues.
which of the above is correct?

2) It's the output using the -oa option.

HEADER    frame t= 0.000
REMARK    THIS IS A SIMULATION BOX
CRYST1   79.230   79.230   79.230  90.00  90.00  90.00 P 1           1
MODEL        0
ATOM      1  CA  GLY     1      -1.847  -2.875  13.644  1.00  0.00
ATOM      2  CA  GLY     1      -4.658   0.117   2.214  1.00  0.00
ATOM      3  CA  GLY     1      -7.470   3.108  -9.215  1.00  0.00
ATOM      4  CA  GLY     2       1.847   2.875  12.859  1.00  0.00
ATOM      5  CA  GLY     2       4.658  -0.117  -2.214  1.00  0.00
ATOM      6  CA  GLY     2       7.470  -3.108 -17.287  1.00  0.00
TER
ENDMDL

Can Someone please explain to me this output format????

why do i get GLY residue for every helix range????

I am not very sure...Someone please shed some light into this.

Thank you.
-- 
Dilraj Lama,
PhD Student,
c/o Dr. R. Sankararamakrishnan,
Bioinformatics and Biomolecular Simulation Lab,
Dept. of BSBE,IIT-Kanpur,
UP-208016:India
email:dennis at iitk.ac.in;dilraj2002 at yahoo.com
mob:09415473973