[gmx-users] analysing ndx file of g_hbond

raja raja_28 at fastmail.us
Wed Jun 28 14:23:52 CEST 2006

Hi Erik Marklund,
Thanks for your suggestions. Your idea of merging index file solved my
immediate problem and now I could at least being able to short list main
chain atoms in the large set of hbonds list.

With thanks!

On Wed, 28 Jun 2006 13:49:59 +0200, "Erik Marklund"
<erikm at xray.bmc.uu.se> said:
> 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
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  raja_28 at fastmail.us

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