[gmx-users] how to make h-bond existence map?
minnale
minnale_gnos at rediffmail.com
Wed Sep 3 09:54:52 CEST 2008
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.
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/1050715198 at Middle5/2206641_2199021/2201650/1?PARTNER=3&OAS
> > >>_QUERY=null>
> > >>
> > >>
> > >>------------------------------------------------------------------------
> > >>
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> > >
> > >-- ========================================
> > >
> > >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
>-------------------------------------------------------------------------------
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