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 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/signature-home.htm/[EMAIL >> PROTECTED]/2206641_2199021/2201650/1?PARTNER=3&OAS_QUERY=null> >> >> >>------------------------------------------------------------------------ >> >>_______________________________________________ >>gmx-users mailing list gmx-users@gromacs.org >>http://www.gromacs.org/mailman/listinfo/gmx-users >>Please search the archive at http://www.gromacs.org/search before posting! >>Please don't post (un)subscribe requests to the list. Use the www interface >>or send it to [EMAIL PROTECTED] >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >-- ======================================== > >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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