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) − 9131 − 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ 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
