[gmx-users] H-bond analysis

[Erik Marklund]

Hi,

I've never used it myself, hut hbplus allegedly uses a more complex hb criterion. http://www.jhu.edu/fleming/Modeling/HBPLUS.html

Kind regards,
Erik

On 17 Apr 2014, at 10:38, michael.b <mbx0009 at yahoo.com> wrote:

> 
> hi,
> 
> I try to analyze H-bonds in an MD trajectory.
> when i look at the definition of an H-bond used by g_hbond it appears
> that only three atoms (acceptor, donor, hydrogen, ADH) are used
> in the analysis performed by this program ... however, i would assume that
> in fact 4 (or up to 6) atoms should be considered because the existence and
> the strength of an H-bond not only depend on the A-D distance and
> the ADH angle  but also on the orientation of the lone pairs of the
> acceptor, and the latter are actually determined by the geometry of
> the atom(s), call them X, the acceptor is covalently bound to, aren't they?
> 
> So, in short, my question is: is anybody aware of a tool that
> can analyze the H-bonds in MD trajectories considering not only
> A-D distance and ADH angle but also the position of X (basically
> the dihedral DHAX) ?
> 
> thanks for any hints
> cheers,
> michael
> 
> 
> 
> 
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