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
--
========================================
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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