[gmx-users] About the %SS values in the output of do_dssp

[Justin A. Lemkul]

sa wrote:
> Dear All,
> 
> I have simulated 6 peptides (with 7 AA each capped in N and C termini) 
> in water and trehalose. During all the simulation time, the six peptides 
> have  b-sheet conformations. I would like  to calculate the average % of 
> secondary structure for the 6 peptides over the course of run. So I have 
> read the subject reported in the following link 
> http://redmine.gromacs.org/issues/683 and used the following command for 
> the two first frames
> 
> 
>        /work/sa001/gmx-post4.5.3/bin/do_dssp_mpi -f *-Center_All.xtc -s
>       run_1.tpr -tu ps -dt 1 -b 1 -e 5 -o
>       6_Peptide_53A6_Trehal_Pref_SS.xpm -sss
>       6_Peptide_53A6_Trehal_Pref_HEBT.dat -ssdump
>       6_Peptide_53A6_Trehal_Dump_SS.dat -sc test.xvg
> 
> I obtained the following output for my six peptides
> 
> @TYPE xy
> @ subtitle "Structure =  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  
> +  +  +  +  +  +  +  +  +  +  +  + B-Sheet +  +  +  +  +  + "
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "Structure"
> @ s1 legend "Coil"
> @ s2 legend "B-Sheet"
> @ s3 legend "Chain_Separator"
>        2    30    12    30     5
>        4    30    12    30     5
> # Totals    60    24    60    10
> # SS %    0.64  0.26  0.64  0.11
> 
> 
> I can understand how the %SS values are obtained in the example given in 
> http://redmine.gromacs.org/issues/683, but not in my case. Could you 
> tell me how the %SS is obtained the output above.
> 

Like any other average.  From the code:

     /* now print percentages */
     fprintf(fp, "%-8s %5.2f", "# SS %", total_count / (real) (mat->nx * mat->ny));
     for(s=0; s<mat->nmap; s++)
     {
         fprintf(fp," %5.2f",total[s] / (real) (mat->nx * mat->ny));
     }
     fprintf(fp,"\n");

So the total number of secondary structure elements is divided by the product of 
(number of frames * number of total residues).

Your results are affected by the problem I mentioned in the issue report you 
quote.  You have 42 residues, but since chain separators count as residues, the 
calculations are all done out of 47 residues instead.  You'll have to either 
modify the code to account for this problem or simply re-calculate the averages 
yourself.

-Justin

> Thank you in advance for your help
> 
> SA
> 
> 
> 

-- 
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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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