[gmx-users] g_hbond

[Justin A. Lemkul]

Steven Neumann wrote:
> 
> 
> On Wed, Aug 31, 2011 at 3:44 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Steven Neumann wrote:
> 
> 
> 
>         On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto: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
>            MILES-IGERT Trainee
>            Department of Biochemistry
>            Virginia Tech
>            Blacksburg, VA
>            jalemkul[at]vt.edu <http://vt.edu/> <http://vt.edu/> | (540)
>         231-9080 <tel:%28540%29%20231-9080>
>            <tel:%28540%29%20231-9080>
> 
>            http://www.bevanlab.biochem.
>         <http://www.bevanlab.biochem./>____vt.edu/Pages/Personal/justin
>         <http://vt.edu/Pages/Personal/justin>
>            <http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>         <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>>
> 
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> 
>          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.
> 
> 
>     I forgot to mention in the previous message that there is no value
>     in summing the hydrogen bonds over time.  Some of those H-bonds may
>     be distinct, and others may be the same H-bond that has broken and
>     subsequently re-formed.  I doubt anyone would find real value in
>     saying that 10 ligands formed 1872 H-bonds with glycine over a
>     trajectory.
> 
>     -Justin
> 
> Obviosuly, but it can provide you some information about binding 
> affinity - some ligands remains close to some residues longer than the 
> others so by sum of this values you can assess residues with higher 
> binding affinity.
>  

The average number of hydrogen bonds over time will tell you the same thing, 
with much greater precision.  There are a maximum number of H-bonds that glycine 
can participate in, since it only has backbone groups to contribute, so if you 
find that, on average, there are 2.5 out of a possible 3 H-bonding sites 
occupied, then yes, it is a strong interaction.  Using some non-physical metric 
will probably get you in trouble with reviewers.  It's up to you to justify what 
you're doing, but summing potentially redundant information doesn't make sense 
to me.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================