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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