[gmx-users] Re: the output of do_dssp

[Hsin-Lin]

Hi, Justin:

Thank you for your reply.
I try to select the group, 'mainchain', when prompted, and get the quantity
of coil still larger than the number of residues of my protein.
The data is the same as the output that generated by the selection, "1.
Protein".
If I select backbone, I get the fatal error: 
Failed to execute command: /Prousr/statphys/hsinlin/dssp/dsspcmbi -na
ddhIPvCe ddJ6Yv7a > /dev/null 2> /dev/null 

And I don't understand even if I can run the selection, "backbone",
successfully.
According the dssp web of wiki:
http://en.wikipedia.org/wiki/DSSP_%28protein%29
the hydrogen bonds are dicided by O, C, H, and N four atoms.
How can we get dssp analysis by backbone that includes only NCCNCCNCC.....?

Sincerely yours,
Hsin-Lin
> 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