[gmx-users] g_hbond

[Justin A. Lemkul]

Steven Neumann wrote:
> 
> 
> On Wed, Aug 31, 2011 at 3:38 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.
>         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
> 
>     In this case number of collisions has to include number of hbonds.
>     If collision is counted as a distance <3.5 and hbond distance <3.5
>     plus angle D-H-A means that collisions covers hbonds... Explain
>     please whether I am wrong.
> 

The second column lists the number of atom pairs that satisfy the distance 
requirement but do not satisfy the angle requirement and therefore are not 
hydrogen bonds.  The two columns are mutually exclusive.  The sum of these two 
columns would be the total number of pairs that are within hydrogen-bonding 
distance, but the first column indicates those that are actually involved in 
hydrogen bonds (because of the angle), and the second column indicates those 
that are not involved in hydrogen bonds.

-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

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