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/683and 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.
Thank you in advance for your help
SA
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