[gmx-users] how to make h-bond existence map?

Wed Sep 3 11:11:00 CEST 2008

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) âˆ’ 9131 âˆ’ 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
-------------------------------------------------------------------------------