[gmx-users] g_hbond and hydrogen bonds involving sulfur

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 15 15:49:15 CEST 2009

Diana Lousa wrote:
> Dear all,
> Does any know why g_hbond does not (at least in a straightforward way) 
> enable the calculation of hbonds involving sulfur atoms (e.g. between 
> cysteines and other residues)? Is there an easy way to tell gromacs to 
> consider sulfur a donor and acceptor atom?

The program probably doesn't consider -SH groups in hydrogen bond analysis 
because in protein structures, the vast majority of hydrogen bonds occur among 
C=O, -NH, and -OH groups in the protein and within the surrounding (usually 
aqueous) solvent.

The only way to get g_hbond to recognize sulfur is to change the code, but this 
is not what I would necessarily call "easy."

As an alternative, since g_hbond calculates geometric parameters (distances and 
angles between the donors and acceptors) to determine the presence or absence of 
a hydrogen bond, you could probably accomplish a similar analysis by using 
g_dist and g_angle for craftily-derived index groups.  Some non-Gromacs 
post-processing would also be involved, as far as determining if the angle and 
distance requirements are met (easily done with Perl, for example).  I realize 
this is more tedious, but it makes such an analysis possible without modifying 
the code.


> Thanks in advance
> Diana Lousa
> -- 
> Diana Lousa
> PhD student
> Protein Modeling Laboratory
> Oeiras, Portugal
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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