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

minnale minnale_gnos at rediffmail.com
Wed Sep 3 07:53:36 CEST 2008


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?
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?
>>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
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