[gmx-users] g_hbond and hydrogen bonds involving sulfur
dlousa at itqb.unl.pt
Thu Oct 15 20:09:18 CEST 2009
Protein Modelling Laboratory
Instituto de Tecnologia Química e Biológica
Universidade Nova de Lisboa
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
>> Thanks in advance
>> Diana Lousa
>> Diana Lousa
>> PhD student
>> Protein Modeling Laboratory
>> Oeiras, Portugal
>> gmx-users mailing list gmx-users at gromacs.org
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www interface
>> or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
More information about the gromacs.org_gmx-users