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.
-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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