[gmx-users] how to make h-bond existence map?
minnale
minnale_gnos at rediffmail.com
Wed Sep 3 15:47:23 CEST 2008
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/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
> > >--------------------------------------------------------------------------
> > >-----
>
>
>
>--
>-------------------------------------------------------------------------------
> 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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