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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