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