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.
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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