<P>
<BR>
Thanks Florian for your detailed reply <BR>
when I mentioned -r and -a options in g_hbond command its showing<BR>
Fatal error:<BR>
Expected a real argument for option -a<BR>
similar error showing when I mentioned cutoff radius(-r) or cutoffangle<BR>
(-a)<BR>
Could you please suggest me<BR>
Thanks in advance.<BR>
On Wed, 03 Sep 2008 Florian Haberl wrote :<BR>
>Hi,<BR>
><BR>
>On Wednesday, 3. September 2008, minnale wrote:<BR>
> > Thanks Justin for your valuable suggestions<BR>
> > I have done the way you suggested. I gave command like this<BR>
> > g_hbond -f .xtc -s .tpr .ndx(contain 5 residues mainchain+H 25 atoms) -num<BR>
> > .xvg -hbm .xpm it showed<BR>
> > Select a group: 15<BR>
> > Selected 15: 'MainChain+H_&_r_22_50_56_121_22'<BR>
> > Select a group: 15<BR>
> > Selected 15: 'MainChain+H_&_r_22_50_56_121_22'<BR>
> > Calculating hydrogen bonds in MainChain+H_&_r_22_50_56_121_22 (25 atoms)<BR>
> > Found 4 donors and 8 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>
> > No hydrogen bonds found!!<BR>
> > Average number of hbonds per timeframe 0.000 out of 16 possible<BR>
> ><BR>
> > gcq#307: "Interfacing Space and Beyond..." (P. J. Harvey)<BR>
> ><BR>
> > It displayed there is no Hydrogen bonds in selected mainchain+H residues.<BR>
> > but it showed 4 donors and 8 acceptors, that doesnt mean that its having<BR>
> > H-bond? Later<BR>
><BR>
>This means that only in principle there are donors and acceptors around but if<BR>
>the distance or angle is not correct than g_hbond will not find any (formed)<BR>
>hbond.<BR>
><BR>
>you can try g_hbond with the option -r and -a to change cutoff radius and<BR>
>cutoff angle but this are the standard criteria for an h-bond.<BR>
><BR>
>greetings,<BR>
><BR>
>Florian<BR>
><BR>
> > when I tried to convert .xpm to .eps by using command<BR>
> > xpm2ps -f .xpm -o .eps it showed<BR>
> > Floating point exception<BR>
> > Can you please give me your kind suggestion<BR>
> ><BR>
> > Thanks in advance.<BR>
> ><BR>
> > On Wed, 03 Sep 2008 Justin A.Lemkul wrote :<BR>
> > >minnale wrote:<BR>
> > >> Hi all,<BR>
> > >> I am confusing while calculating hydrogen bonds of my protein.I issued<BR>
> > >> this command g_hbond -f .xtc -s .tpr -num .xvg I didnt mention .ndx<BR>
> > >> because I wanted to know the H-bonds in whole protein system. I have<BR>
> > >> 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 Will do grid-seach on 16x16x16 grid,<BR>
> > >> rcut=0.35 Reading frame 37000 time 7400.000 Average number of hbonds<BR>
> > >> per timeframe 81.692 out of 30175 possible gcq#295: "It Just Tastes<BR>
> > >> 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>
> > ><BR>
> > >For calculating H-bonds within the MainChain, yes. You have not<BR>
> > > determined all of the H-bonds in the protein, however, because you are<BR>
> > > not including side chains in the calculation.<BR>
> > ><BR>
> > >>2. how can I make h-bond existence map?<BR>
> > ><BR>
> > >Is g_hbond -hbm not what you want?<BR>
> > ><BR>
> > >-Justin<BR>
> > ><BR>
> > >>3. For this is it require to write programming or script?<BR>
> > >><BR>
> > >><BR>
> > >><BR>
> > >>Rediff Shopping<BR>
> > >> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/sign<BR>
> > >>ature-home.htm/1050715198@Middle5/2206641_2199021/2201650/1?PARTNER=3&OAS<BR>
> > >>_QUERY=null><BR>
> > >><BR>
> > >><BR>
> > >>------------------------------------------------------------------------<BR>
> > >><BR>
> > >>_______________________________________________<BR>
> > >>gmx-users mailing list gmx-users@gromacs.org<BR>
> > >>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>
> > >>Please search the archive at http://www.gromacs.org/search before<BR>
> > >> posting! Please don't post (un)subscribe requests to the list. Use the<BR>
> > >> www interface or send it to gmx-users-request@gromacs.org. Can't post?<BR>
> > >> Read http://www.gromacs.org/mailing_lists/users.php<BR>
> > ><BR>
> > >-- ========================================<BR>
> > ><BR>
> > >Justin A. Lemkul<BR>
> > >Graduate Research Assistant<BR>
> > >Department of Biochemistry<BR>
> > >Virginia Tech<BR>
> > >Blacksburg, VA<BR>
> > >jalemkul[at]vt.edu | (540) 231-9080<BR>
> > >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>
> > ><BR>
> > >========================================<BR>
><BR>
><BR>
><BR>
>--<BR>
>-------------------------------------------------------------------------------<BR>
> Florian Haberl<BR>
> Computer-Chemie-Centrum<BR>
> Universitaet Erlangen/ Nuernberg<BR>
> Naegelsbachstr 25<BR>
> D-91052 Erlangen<BR>
> Telephone: +49(0) − 9131 − 85 26573<BR>
> Mailto: florian.haberl AT chemie.uni-erlangen.de<BR>
>-------------------------------------------------------------------------------<BR>
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