[gmx-users] Helicity

[Justin Lemkul]

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
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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