[gmx-users] how to use the triplets index file generated by g_hbond

Justin A. Lemkul jalemkul at vt.edu
Sat May 5 19:43:01 CEST 2012

On 5/5/12 1:22 PM, Yun Shi wrote:
> Hello all,
> I have used g_hbond with -hbn option to generate a .ndx file that has Acceptor -
> Donor - Hydrogen in each line of the last index group.
> But I wonder I could I use this index file to monitor each hydrogen bond
> specified by these triplets along the trajectory?

Depending on what you're trying to do, you can map the triplets in hbond.ndx 
with the hbmap.xpm file to obtain, for instance, the % of total frames that a 
particular hydrogen bond exists.  I've done something along those lines with a 
script I call plot_hbmap.pl, available from:


Please note the usage information in the header of the file.

> Also, I understand that the -ins in no longer available. But how can we analyze
> those water-mediated hydrogen bonds?

Doing something like this will require careful use of index groups and external 
scripting.  Presumably, if you have two groups (let's call them A and B), if 
group A forms hydrogen bonds to a certain group of SOL residues, and if group B 
does the same, with some of those SOL molecules overlapping in some given 
frames, you can make an argument for a water-mediated hydrogen bond. 
Determining the existence of the hydrogen bonds is easy with g_hbond and index 
groups.  Determining simultaneous occurrence requires an external script, and 
can make use of hbmap.xpm (to determine which frames contain the hydrogen bonds) 
and hbond.ndx (to determine which groups are participating in those hydrogen bonds).



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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