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