[gmx-users] analysing ndx file of g_hbond
erikm at xray.bmc.uu.se
Wed Jun 28 16:59:06 CEST 2006
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?
> > 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
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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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