[gmx-users] Re: the output of do_dssp

[Justin A. Lemkul]

Hsin-Lin wrote:
> Hi, Justin
> 
> 
> 
> Thank you for your patience.
> 
> According your reply, I used trjconv to write only protein group into another
> file.
> 
> I execute do_dssp again in group “protein”and “mainchain” respectively but
> still get coils more than total residues.
> 

Can you post the text of your coordinate file (preferably not as an attachment, 
just copy and paste it into an email)?

-Justin

> Why?
> 
> 
> 
> Hsin-Lin
> 
> 
> 
> 
> 
> 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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