[gmx-users] the output of do_dssp

[Justin A. Lemkul]

Hsin-Lin wrote:
> Hi,
> 
> I use do_dssp to generate xvg file collect the last line to make a plot.
> There are something written in this way:
> ------------------
> @ s0 legend "Structure"
> @ s1 legend "Coil"
> @ s2 legend "Bend" 
>     0    5    14   1
> -------------------
> My system is dimer and each peptide has 6 residue.

Then you have a problem.  Your output indicates 14 residues are in a random 
coil, so either you have more than 12 total residues, or something went wrong in 
the dssp calculation.

> And the number I choose to analyze is "1. Protein".
> 

Perhaps this is why you had a problem.  Normally, choosing "Protein" would cause 
the calculation to hang, but maybe that is not the case any more.  See here for 
the proper group to choose and the rationale:

http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp

> Now I have a question, if I want to calculate the percentage of secondary
> structure.
> In the example above, is it calculated in this way 5/12=42%?
> 

I'd question your results first...you don't have 12 residues in your 
calculation, otherwise your protein is 14/12 = 117% random coil!  Also realize 
that (by default) the "Structure" term only includes alpha helix, beta strand, 
bend, and turn.  Other structural elements are not included.  That may or may 
not be what you want, depending on the structural elements of your protein.

-Justin

> Hsin-Lin
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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