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

[Justin A. Lemkul]

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

========================================