Hsin-Lin wrote:
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.
Then some other elements of your system are being detected as containing
relevant atoms. What happens if you run do_dssp on a single structure
containing only your 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.
No, you can't.
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.....?
You can't - DSSP requires the presence of the carbonyl O in order to determine
hydrogen bonding geometry. If you don't have a full carbonyl, the analysis fails.
-Justin
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
--
========================================
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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