[gmx-users] g_hbond and hydrogen bonds involving sulfur

[Diana Lousa]

Diana Lousa
Protein Modelling Laboratory
Instituto de Tecnologia Química e Biológica
Universidade Nova de Lisboa
Portugal

On Thu, 15 Oct 2009, Justin A. Lemkul wrote:

>
>
> 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.
>
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.

> 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.
>
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

> -Justin
>
>> 
>> Thanks in advance
>> 
>> Diana Lousa
>> 
>> -- 
>> Diana Lousa
>> PhD student
>> Protein Modeling Laboratory
>> ITQB/UNL
>> 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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