Thanks to Florain for prompt reply May be this is trivial query to you I have done in this way 1. Making index file make_ndx -f .gro -o .ndx selected 7(mainchain+H)& r 24 26 45 67 78 the index showed like this [ MainChain+H_&_r_22_50_56_121_22 ] 370 370 371 371 372 372 386 386 387 387 822 823 824 838 839 916 917 918 932 933 1839 1840 1841 1855 1856
2. g_hbond -f .xtc -s .tpr -n .ndx -num .xvg -hbm .xpm -r 0.35 -a 30 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 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. 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. Thanks in advance On Wed, 03 Sep 2008 Florian Haberl wrote : >Hi, > >On Wednesday, 3. September 2008, minnale wrote: > > Thanks Florian for your detailed reply > > when I mentioned -r and -a options in g_hbond command its showing > > Fatal error: > > Expected a real argument for option -a > > similar error showing when I mentioned cutoff radius(-r) or cutoffangle > > (-a) > > Could you please suggest me > > Thanks in advance. > >try > >g_hbond -h > >You must enter other values, but be careful the default options are normally >the standard onces. > >Take also a look on your structure, if all residues you want to analyse are in >your index group! > >Greetings, > >Florian > > > > > > On Wed, 03 Sep 2008 Florian Haberl wrote : > > >Hi, > > > > > >On Wednesday, 3. September 2008, minnale wrote: > > > > 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 > > > > > >This means that only in principle there are donors and acceptors around > > > but if the distance or angle is not correct than g_hbond will not find > > > any (formed) hbond. > > > > > >you can try g_hbond with the option -r and -a to change cutoff radius and > > >cutoff angle but this are the standard criteria for an h-bond. > > > > > >greetings, > > > > > >Florian > > > > > > > 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/ > > > > >>sign > > > > >> ature-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 > > > > > > > > > >======================================== > > > > > >-- > > >-------------------------------------------------------------------------- > > >----- Florian Haberl > > > Computer-Chemie-Centrum > > > Universitaet Erlangen/ Nuernberg > > > Naegelsbachstr 25 > > > D-91052 Erlangen > > > Telephone: +49(0) â 9131 â 85 26573 > > > Mailto: florian.haberl AT chemie.uni-erlangen.de > > >-------------------------------------------------------------------------- > > >----- > > > >-- >------------------------------------------------------------------------------- > Florian Haberl > Computer-Chemie-Centrum > Universitaet Erlangen/ Nuernberg > Naegelsbachstr 25 > D-91052 Erlangen > Telephone: +49(0) â 9131 â 85 26573 > Mailto: florian.haberl AT chemie.uni-erlangen.de >-------------------------------------------------------------------------------
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