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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