[gmx-users] g_hbond and hydrogen bonds involving sulfur

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Oct 15 21:01:07 CEST 2009

Hi Diana,

> Well, minorities should not be disregarded just because they are poorly
> represented...In some cases a rare event makes all the difference. I think
> it would be helpeful to have the possiblity to calculate S-H...X bonds or
> X-H...S bonds with g_hbond.

In many cases these tools come about on a per-need-implementation
basis. You or any of your colleagues is most welcome to provide a
modification of g_hbond that will calculate hydrogen bonds other than
O|N-H-O|N. You can't really expect somebody to just invest time to
make your life easy, without profit for him/herself.

> We found a simple, although, not very elegant way to get around the
> question. What we did was to create a topology, for hbond calculation
> purposes only, where SG in a given cysteine was replaced by an OG. Basicaly,
> we used a sulfur disguised of oxigen, what an atom has to do to be accepted
> as one of the guys :P

This assumes that the geometrical criteria for hydrogen bonds
involving sulfur are equal to those involving oxygen and/or nitrogen.
But is that true? Sulfur is much larger and has much more
delocalization of charge. This will alter the properties of hydrogen
bonds. For instance, the hydrogen bond is much weaker, ergo has a much
shallower potential well, and will thus have a broader distribution
that might be considered 'hydrogen bond'. On the other hand, the
weakness might actually call for a stricter definition. The angle will
definitely have a broader range, because of delocalization of
electrons over the atomic surface.

It's not that easy...

But that's just my two cents.



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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