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
>> >
>> >========================================
>>
>>
>>
>>
>>------------------------------------------------------------------------
>>
>>_______________________________________________
>>gmx-users mailing list gmx-users@gromacs.org
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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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