[gmx-users] g_hbond

[Justin A. Lemkul]

Steven Neumann wrote:
> 
> 
> On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul <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/> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     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

> 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 right? 
>  
> Steven
> 

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

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

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