[gmx-users] g-hbond and N acceptors
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
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