[gmx-users] g-hbond and N acceptors

Michel Cuendet michel.cuendet at isb-sib.ch
Tue Nov 13 19:54:21 CET 2007


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...

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 ?



Michel Cuendet, Ph.D
Molecular Modeling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne

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