[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>
> 
>     ==============================__==========
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto: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
>     <mailto: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 right? 
>  

No.  The second column is not inclusive of the first.  It counts the number of 
atoms that are within hydrogen bonding distance, but do not meet the criteria 
because of the angle between D-H-A.

-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

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