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<BR>
Thanks Justin for your quick reply<BR>
the g_hbond command ran succesfully and gave me .xvg file and it contain 3 columns <BR>
that is like<BR>
<BR>
@ title "Hydrogen Bonds"<BR>
@ xaxis label "Time"<BR>
@ yaxis label "Number"<BR>
@TYPE xy<BR>
@ view 0.15, 0.15, 0.75, 0.85<BR>
@ legend on<BR>
@ legend box on<BR>
@ legend loctype view<BR>
@ legend 0.78, 0.8<BR>
@ legend length 2<BR>
@ s0 legend "Hydrogen bonds"<BR>
@ s1 legend "Pairs within 0.35 nm"<BR>
0 79 674<BR>
0.2 87 687<BR>
0.4 80 693<BR>
0.6 69 690<BR>
0.8 79 691<BR>
1 74 690<BR>
1.2 81 700<BR>
1.4 75 681<BR>
1.6 83 687<BR>
<BR>
the first column is time then could please tell about 2nd and 3rd columns<BR>
Thanks in advance.<BR>
<BR>
On Thu, 28 Aug 2008 Justin A.Lemkul wrote :<BR>
><BR>
><BR>
>minnale wrote:<BR>
>> Hi all,<BR>
>> 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<BR>
>>g_hbond -f .xtc -s .tpr -n .ndx(Index file contain all residues mainchain+H atoms) -num .xvg -g .log<BR>
>>its showed<BR>
>><BR>
>>Program g_hbond, VERSION 3.3.1<BR>
>>Source code file: statutil.c, line: 799<BR>
>><BR>
>>Invalid command line argument:<BR>
>>-g<BR>
>><BR>
>>Can you please tell where I have done mistake?<BR>
>>Thanks in advance for your valuable suggestions.<BR>
>><BR>
>><BR>
><BR>
>The error tells you exactly what the problem is. There is no such option. The -g flag appears in newer versions of Gromacs.<BR>
><BR>
>-Justin<BR>
><BR>
>><BR>
>><BR>
>>------------------------------------------------------------------------<BR>
>><BR>
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><BR>
>-- ========================================<BR>
><BR>
>Justin A. Lemkul<BR>
>Graduate Research Assistant<BR>
>Department of Biochemistry<BR>
>Virginia Tech<BR>
>Blacksburg, VA<BR>
>jalemkul[at]vt.edu | (540) 231-9080<BR>
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>
><BR>
>========================================<BR>
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