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

[sa]

Ok Thank you Justin for this clarification



>
>
>
> 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
> >
> >
> >
>
> --
> ========================================
>
> 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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