[gmx-users] G_hbond's hydrogen bond ordering?

Danny Neil magicmandan at gmail.com
Tue Nov 13 19:28:53 CET 2007

Hello -

I am working on analyzing the output of g_hbond, and I am having some
conflicting results regarding the ordering of the -hbn output index
file.  I'm using the results of the -g .log file to index the bonds in
the .xpm existence map, but these don't seem to correlate.  In
essence, I'm curious why the first line of the log file:

PHE99N        PHE99H       PRO100O
[first line of hbond.log file]

doesn't correspond to:


  oo                      oooo   oo
[first line of hbmap.xpm, existence map file].

The atom names as they are set up in the log file are important to me
- having "PHE99N" is more useful than just the number "1898."  Is
there any way I can make the log file reflect the ordering of the
index file, or can I use the log file as the index file?



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