[gmx-users] g_hbond

Steven Neumann s.neumann08 at gmail.com
Wed Aug 31 16:30:41 CEST 2011

On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> Steven Neumann wrote:
>> Hi Gromacs Users,
>>  I have calculated hydrogen bonds and collisions between my ligands and
>> every single residue using g_hbond. Looking at the criteria adpoted by
>> Gromacs I found impossible that number of hydrogen bonds were higher than
>> number of collisions... And what is interesting in one of my residue I
>> obtained result like this... All Hbonds with Glycine - 1872, All Collisions
>> 704.
>>  Does anyone know how is it possible?
> I don't know how any of your numbers are possible (1872 H-bonds forming
> with a glycine?), or what you are defining as a collision and how you
> calculated it. Please provide the exact commands that you're using.  If
> you're equating a contact (e.g. from g_mindist) with a collision, then
> realize that the default criteria for a contact are very different than the
> geometric criteria for a hydrogen bond.
> -Justin
> --
> ==============================**==========
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/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/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>

My system is made of 10 ligands and one protein. I used command:

g_hbond -f md.trr -s md.tpr -n res91.ndx -num 91with10LIGbonds.xvg

Where I specified in the index file two groups: 10 ligands and Glycine
residue. So I have calculated hbonds (second column) and collisions (third
column) and then I made a sum of all frames during 100 ns simualtion time
(one frame every 50 ps) obtaining 1872 hbonds and 703 collisions between
Glycine and 10 ligands. I did it with every residue to assess binding
affinity of different amino acids.
Criteria for collision is distance <3.5 A, and fo hbond distance <3.5 A and
angle. So when calcualting hbond and collisions the number of hbonds has has
to be smaller while collision takes into account hbonds as welll. I obtained
results like this for all other residues which seems to be correct. Am I

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110831/fc2e61f9/attachment.html>

More information about the gromacs.org_gmx-users mailing list