[gmx-users] query on using g_bundle

[Dilraj Lama]

hello gmx-users,
                This is my second post on the same subject as I have got no response for my
previous post..If I was not very clear the first time round,i will try to refresh
my queries.I hope to get some response this time.

  I have some queries regarding using g_bundle.

My queries are:

1) Suppose I have two helices (Say residue 3-20 and 42-64),Then How do I define my groups in the
index file.Do I have to define the CA atoms of the range 3-20 and 42-64 completely or DO i have to
define only the CA atoms of the First and last residues of the range 3-20 and 42-64 ?????????????

2) Below I show a part of the output file "H1H2.pdb" generated using g_bundle and index groups as
CA atoms from range 3-20 and 42-64.

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

I am not sure about this output.

Why do I see GLY residue???

what are this coordinates???

Can you please help me interprate this output???

Please shed some light on this.

Regards.
-- 
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