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

[Florian Haberl]

Hi,

On Wednesday, 3. September 2008, minnale wrote:
> Thanks Justin for your valuable suggestions
> I have done the way you suggested. I gave command like this
> g_hbond -f .xtc -s .tpr .ndx(contain 5 residues mainchain+H 25 atoms)  -num
> .xvg -hbm .xpm it showed
> Select a group: 15
> Selected 15: 'MainChain+H_&_r_22_50_56_121_22'
> Select a group: 15
> Selected 15: 'MainChain+H_&_r_22_50_56_121_22'
> Calculating hydrogen bonds in MainChain+H_&_r_22_50_56_121_22 (25 atoms)
> Found 4 donors and 8 acceptors
> Reading frame       0 time    0.000
> Will do grid-seach on 16x16x16 grid, rcut=0.35
> Reading frame   37000 time 7400.000
> No hydrogen bonds found!!
> Average number of hbonds per timeframe 0.000 out of 16 possible
>
> gcq#307: "Interfacing Space and Beyond..." (P. J. Harvey)
>
> It displayed there is no Hydrogen bonds in selected mainchain+H residues.
> but it showed 4 donors and 8 acceptors, that doesnt mean that its having
> H-bond? Later

This means that only in principle there are donors and acceptors around but if 
the distance or angle is not correct than g_hbond will not find any (formed) 
hbond.

you can try g_hbond with the option -r and -a to change cutoff radius and 
cutoff angle but this are the standard criteria for an h-bond.

greetings,

Florian

> when I tried to convert .xpm to .eps by using command
> xpm2ps -f .xpm -o .eps it showed
> Floating point exception
> Can you please give me your kind suggestion
>
> Thanks in advance.
>
> On Wed, 03 Sep 2008 Justin A.Lemkul wrote :
> >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?
> >>
> >>
> >>
> >>Rediff Shopping
> >> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/sign
> >>ature-home.htm/1050715198 at Middle5/2206641_2199021/2201650/1?PARTNER=3&OAS
> >>_QUERY=null>
> >>
> >>
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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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 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
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 Telephone:  	+49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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