[gmx-users] g_hbond + invalid command line argument -g

[David van der Spoel]

minnale wrote:
>  
> Thanks Justin for your reply
> I am interested to get file which contain how many hydrogen bonds are 
> there in my protein and the bonds present between which atoms?
> Is there anyway to get this file
> can you please tell me,

g_hbond -h

> Thanks in advance for your kind suggestion 
> 
> On Thu, 28 Aug 2008 Justin A.Lemkul wrote :
>  >
>  >
>  >minnale wrote:
>  >> 
>  >>Thanks Justin for your quick reply
>  >>the g_hbond command ran succesfully and gave me .xvg file and it 
> contain 3 columns
>  >>that is like
>  >>
>  >>@    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
>  >>      0.6          69        690
>  >>      0.8          79        691
>  >>        1          74        690
>  >>      1.2          81        700
>  >>      1.4          75        681
>  >>      1.6          83        687
>  >>
>  >>the first column is time then could please tell about 2nd and 3rd columns
>  >>Thanks in advance.
>  >
>  >Read the header of the file, specifically:
>  >
>  >@ s0 legend "Hydrogen bonds"
>  >@ s1 legend "Pairs within 0.35 nm"
>  >
>  >Gromacs always prints legends for what the data mean.
>  >
>  >-Justin
>  >
>  >>
>  >>On Thu, 28 Aug 2008 Justin A.Lemkul wrote :
>  >>  >
>  >>  >
>  >>  >minnale wrote:
>  >>  >>  Hi all,
>  >>  >>  I am new to gromacs, I am interested in calculate Hydrogen 
> bonds of my protein. So I have issued the *g_hbond command like this
>  >>  >>g_hbond -f .xtc -s .tpr -n .ndx(Index file contain all residues 
> mainchain+H atoms) -num .xvg -g .log
>  >>  >>its showed
>  >>  >>
>  >>  >>Program g_hbond, VERSION 3.3.1
>  >>  >>Source code file: statutil.c, line: 799
>  >>  >>
>  >>  >>Invalid command line argument:
>  >>  >>-g
>  >>  >>
>  >>  >>Can you please tell where I have done mistake?
>  >>  >>Thanks in advance for your valuable suggestions.
>  >>  >>
>  >>  >>
>  >>  >
>  >>  >The error tells you exactly what the problem is.  There is no such 
> option.  The -g flag appears in newer versions of Gromacs.
>  >>  >
>  >>  >-Justin
>  >>  >
>  >>  >>
>  >>  >>
>  >>  
>  >>------------------------------------------------------------------------
>  >>  >>
>  >>  >>_______________________________________________
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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
>  >>  >
>  >>  >========================================
>  >>
>  >>
>  >>
>  >>
>  >>------------------------------------------------------------------------
>  >>
>  >>_______________________________________________
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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
>  >
>  >========================================
> 
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se