<P>
<BR>
Thanks Justin for your reply <BR>
I am interested to get file which contain how many hydrogen bonds are there in my protein and the bonds present between which atoms?<BR>
Is there anyway to get this file <BR>
can you please tell me,<BR>
Thanks in advance for your kind suggestion <BR>
<BR>
On Thu, 28 Aug 2008 Justin A.Lemkul wrote :<BR>
><BR>
><BR>
>minnale wrote:<BR>
>> <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>
>Read the header of the file, specifically:<BR>
><BR>
>@ s0 legend "Hydrogen bonds"<BR>
>@ s1 legend "Pairs within 0.35 nm"<BR>
><BR>
>Gromacs always prints legends for what the data mean.<BR>
><BR>
>-Justin<BR>
><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>
>> >>_______________________________________________<BR>
>> >>gmx-users mailing list gmx-users@gromacs.org<BR>
>> >>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>
>> >>Please search the archive at http://www.gromacs.org/search before posting!<BR>
>> >>Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request@gromacs.org.<BR>
>> >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>
>> ><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>
>><BR>
>><BR>
>><BR>
>><BR>
>>------------------------------------------------------------------------<BR>
>><BR>
>>_______________________________________________<BR>
>>gmx-users mailing list gmx-users@gromacs.org<BR>
>>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>
>>Please search the archive at http://www.gromacs.org/search before posting!<BR>
>>Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request@gromacs.org.<BR>
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>
><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>
</P>
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