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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