[gmx-users] g-hbond and N acceptors

David van der Spoel spoel at xray.bmc.uu.se
Tue Nov 13 20:08:34 CET 2007

Michel Cuendet wrote:
> Hi,
> I'm studying protein-protein interaction, and have done extensive h-bond 
> statistics. I'm still using g_hbond 3.1.4 for compatibility of the angle 
> and distance criteria with older work (and there was at some point a 
> segmentation fault problem with newer versions). Now looking at single 
> occurences of h-bonds, I noticed some weird things : a series of NH2 
> -NH3 encounters between a GLN and a LYS reported as an h-bond, for 
> example...
The new version has been tested by comparing to other programs and gives 
the same results. I am not sure what you are referring to.

> Does the -nitacc option mean that _any_ nitrogen atom is automatically 
> considered an acceptor ? Why would this surprising behavior be set by 
> default ? Only nitrogens with a lone pair of electrons can be acceptors, 
> such as the unprotonated one in histidines. Without the -nitacc option, 
> does g_hbond completely neglect hbonds involving _any_ nitrogen acceptor ?
> Please tell me if I misunderstand something. Or has the behavior of 
> g_hbond been modified in later versions of gromacs regarding the 
> N-acceptor behavior ?
No, this is one of the few points that have not been altered. I guess 
you are correct that Hbonds are not expected for some of these 
interactions, like Gln - Lys. NH2 groups that are not aromatic (amines) 
one accept Hbonds of course. However there is not so much chemical 
knowledge in the program, and to make matters worse, you can not select 
acceptors or donors separately.

> Thanks,
> Michel
> ==========================================================
> Michel Cuendet, Ph.D
> Molecular Modeling Group
> Swiss Institute of Bioinformatics
> CH-1015 Lausanne
> Switzerland
> ==========================================================
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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