[gmx-users] analysing ndx file of g_hbond

[Erik Marklund]

On Wed, 2006-06-28 at 22:37 +0800, Yang Ye wrote:
> Erik Marklund wrote:
> > 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
> >   
> X | Y
> 
> I was making the same mistake and still ask why I couldn't get it.
I'm pretty sure it's supposed to be:

 X & Y

since you don't want to merge the main chain and the hbonds (union of X
and Y = X | Y). Rather, you need to find the intersection of X and Y (=
X & Y). Or haven't I understood your problem correctly?

/Erik Marklund

> >  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
> >>
> >>     
> 
> 
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- 
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