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? 2. how can I make h-bond existence map? 3. For this is it require to write programming or script?
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