<P>
<BR>
Thanks to Florain for prompt reply<BR>
May be this is trivial query to you<BR>
I have done in this way<BR>
1. Making index file <BR>
make_ndx -f .gro -o .ndx<BR>
selected 7(mainchain+H)& r 24 26 45 67 78<BR>
the index showed like this<BR>
[ MainChain+H_&_r_22_50_56_121_22 ]<BR>
370 370 371 371 372 372 386 386 387 387 822 823 824 838 839<BR>
916 917 918 932 933 1839 1840 1841 1855 1856<BR>
<BR>
2. g_hbond -f .xtc -s .tpr -n .ndx -num .xvg -hbm .xpm -r 0.35 -a 30<BR>
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<BR>
atoms) 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>
Then I have given same command but slight change -r 0.25 -a 30 but it showed same data I have pasted above tells no H-bonds found.<BR>
<BR>
Could please suggest me angle cutoff and radius cutoff values.I have tried to get information about these values but I couldnt able to get.<BR>
<BR>
Thanks in advance<BR>
<BR>
On Wed, 03 Sep 2008 Florian Haberl wrote :<BR>
>Hi,<BR>
><BR>
>On Wednesday, 3. September 2008, minnale wrote:<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>
><BR>
>try<BR>
><BR>
>g_hbond -h<BR>
><BR>
>You must enter other values, but be careful the default options are normally<BR>
>the standard onces.<BR>
><BR>
>Take also a look on your structure, if all residues you want to analyse are in<BR>
>your index group!<BR>
><BR>
>Greetings,<BR>
><BR>
>Florian<BR>
><BR>
><BR>
> ><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)<BR>
> > > > -num .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<BR>
> > > > atoms) 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<BR>
> > > > residues. but it showed 4 donors and 8 acceptors, that doesnt mean that<BR>
> > > > its having H-bond? Later<BR>
> > ><BR>
> > >This means that only in principle there are donors and acceptors around<BR>
> > > but if the distance or angle is not correct than g_hbond will not find<BR>
> > > any (formed) 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<BR>
> > > > >> issued this command g_hbond -f .xtc -s .tpr -num .xvg I didnt<BR>
> > > > >> mention .ndx because I wanted to know the H-bonds in whole protein<BR>
> > > > >> system. I have selected mainchain+H two times, command went fine and<BR>
> > > > >> 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<BR>
> > > > >> grid, rcut=0.35 Reading frame 37000 time 7400.000 Average number of<BR>
> > > > >> hbonds per timeframe 81.692 out of 30175 possible gcq#295: "It Just<BR>
> > > > >> 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>
> > > > ><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<BR>
> > > > > are 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/<BR>
> > > > >>sign<BR>
> > > > >> ature-home.htm/1050715198@Middle5/2206641_2199021/2201650/1?PARTNER=<BR>
> > > > >>3&OAS _QUERY=null><BR>
> > > > >><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<BR>
> > > > >> the www interface or send it to gmx-users-request@gromacs.org. Can't<BR>
> > > > >> post? 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>
> > >----- Florian Haberl<BR>
> > > Computer-Chemie-Centrum<BR>
> > > Universitaet Erlangen/ Nuernberg<BR>
> > > Naegelsbachstr 25<BR>
> > > D-91052 Erlangen<BR>
> > > Telephone: +49(0) â 9131 â 85 26573<BR>
> > > Mailto: florian.haberl AT chemie.uni-erlangen.de<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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