[gmx-users] how to make h-bond existence map?

[Justin A. Lemkul]

minnale wrote:
>  
> Hi all,
>   I am confusing while calculating hydrogen bonds of my protein.I issued 
> this command g_hbond -f .xtc -s .tpr -num .xvg
> I didnt mention .ndx because I wanted to know the H-bonds in whole 
> protein system. I have selected mainchain+H two times, command went fine 
> and it showed
> 
> Select a group: 7
> Selected 7: 'MainChain+H'
> Select a group: 7
> Selected 7: 'MainChain+H'
> Calculating hydrogen bonds in MainChain+H (881 atoms)
> Found 170 donors and 355 acceptors
> Reading frame      0 time    0.000 
> Will do grid-seach on 16x16x16 grid, rcut=0.35
> Reading frame  37000 time 7400.000 
> Average number of hbonds per timeframe 81.692 out of 30175 possible
> gcq#295: "It Just Tastes Better" (Burger King)
> 
> It generated .xvg file and it con@    title "Hydrogen Bonds"
> @    xaxis  label "Time"
> @    yaxis  label "Number"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "Hydrogen bonds"
> @ s1 legend "Pairs within 0.35 nm"
>         0          79        674
>       0.2          87        687
>       0.4          80        693
>         .
>         .
>         .
>           .
>           .
>         etc
> 
> 1.Could you please tell me the way I have done was correct or not?

For calculating H-bonds within the MainChain, yes.  You have not determined all 
of the H-bonds in the protein, however, because you are not including side 
chains in the calculation.

> 2. how can I make h-bond existence map?

Is g_hbond -hbm not what you want?

-Justin

> 3. For this is it require to write programming or script?
> 
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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