[gmx-users] Re: the output of do_dssp

[Justin A. Lemkul]

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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