Dear All, <br><br>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 <a href="http://redmine.gromacs.org/issues/683">http://redmine.gromacs.org/issues/683</a> and used the following command for the two first frames <br>
<h3> /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<br>
</h3>I obtained the following output for my six peptides<br><br>@TYPE xy<br>@ subtitle "Structure = + + + + + + + + + + + + + + + + + + + + + + + + + + + + B-Sheet + + + + + + "<br>
@ view 0.15, 0.15, 0.75, 0.85<br>@ legend on<br>@ legend box on<br>@ legend loctype view<br>@ legend 0.78, 0.8<br>@ legend length 2<br>@ s0 legend "Structure"<br>@ s1 legend "Coil"<br>@ s2 legend "B-Sheet"<br>
@ s3 legend "Chain_Separator"<br> 2 30 12 30 5<br> 4 30 12 30 5<br># Totals 60 24 60 10<br># SS % 0.64 0.26 0.64 0.11<br><br><br>I can understand how the %SS values are obtained in the example given in <a href="http://redmine.gromacs.org/issues/683">http://redmine.gromacs.org/issues/683</a>, but not in my case. Could you tell me how the %SS is obtained the output above.<br>
<br>Thank you in advance for your help<br><br>SA<br><br><br><br>