[gmx-users] Helicity

[shivangi nangia]

Thanks a lot!



<jalemkul at vt.edu> wrote:

>
>
> On 2/6/15 3:42 PM, shivangi nangia wrote:
>
>> Thanks. I am aware of all those commands.
>>
>> My question is specific to gromacs out, the file helicity.xvg has an
>> output
>> of the form:
>>
>>    9 @    title "Helicity per Residue"
>>   10 @    xaxis  label "Residue"
>>   11 @    yaxis  label "% of time"
>>   12 @TYPE xy
>>   13          1           0
>>   14          2     92.6148
>>   15          3     86.8263
>>   16          4      96.008
>>
>> ..........................so on
>>
>> It is telling me residue 2 is 92 % of time (that I specified) helical.
>>
>> I want the average helicity of the peptide during the specified time.
>>
>>
> The proper tool for this is do_dssp.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
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> University of Maryland, Baltimore
> 20 Penn St.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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