[gmx-users] about g_hbond

Justin A. Lemkul jalemkul at vt.edu
Wed May 11 17:10:57 CEST 2011

lina wrote:
> Hi,
> For group A, b, C.
> It's no doubt can get hb forming number between A-b, b-C. b-(A or C).
> But I don't know how to get the number of residues of b forming both
> with A and B at the same time. namely b-A&C, not with AC group.

There's no direct way to do it, but from the output files of g_hbond it can be 
done.  You'd need the .xpm files of A-C and B-C hydrogen bonds, and write some 
script that parses the .xpm files, and whenever there is an entry of A-C in the 
same frame as B-C, then you have a hydrogen bond mediated between the two. 
There's lots of discussion in the list archive about water-mediated hydrogen 
bonds that is likely applicable here.

Note that if you're using g_hbond in version 4.5, there is an important bug that 
was fixed just yesterday:



> Thanks,
> --
> Best Regards,
> lina


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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