[gmx-users] analysing ndx file of g_hbond

[Erik Marklund]

On Wed, 2006-06-28 at 04:29 -0700, raja wrote:
> Dear all,
> 
> The index file produced by g_hbond listing many rows of hbonds making
> atoms combination. Is there a way to get the corresponding residue and
> atom name for those numbers by any of the gromacs program or if anyone
> having the script to do that, kindly pass it on to me. My primary
> objective is to know how many hbond listed in index file are belong to
> main chain atoms.
> 

How about using make_ndx? Try the following:
 X & Y
 q
X being the index group containing the h-bonds and Y being the main
chain index group. You will probably have to merge the g_hbond index
file with an index file of your system first.

Atom names and residues is slightly more problematic. I recommend using
awk within a cshell (any shell would do) script to extract such
information from a .gro-file of your system. Just loop through the
g_hbond index file and have awk print atom names, residues, or whatever.

Note that the ndx-file from h_bond is NOT merged (if I remember this
correctly), so a-d-pairs are likely to show up several times in your
index file. Depending on how you choose to use the index file, this
could cause problems. This bug, along with a few other oddities, was
fixed in the latest cvs version of g_hbond.

/Erik Marklund

> With thanks!
> B.Nataraj
> -- 
>   raja
>   raja_28 at fastmail.us
> 
-- 
Erik Marklund, PhD Student, Molecular Biopcysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4537          fax: 46 18 511 755
erikm at xray.bmc.uu.se