Dear Gromacs users,
I used do_dssp to calculate the secondary structure of peptide. From
the output scount.xvg file, the last column shows the number of
residues that is "chain separator". At the end of the scount.xvg file,
the last line provide the percentage of different secondary
structures. The unusual is the normalization includes the "chain
separator" column (see a example below). This seems like an error. Is
there any other suggestion? I re-calculate the percentage of various
secondary structures and leave the "chain separator" out.
Thank you,
Loan
For example:
# do_dssp is part of G R O M A C S:
#
# GROwing Monsters And Cloning Shrimps
#
@ title "Secondary Structure"
@ xaxis label "Time (ps)"
@ yaxis label "Number of Residues"
@TYPE xy
@ subtitle "Structure = + + + Turn"
@ 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 "Bend"
@ s3 legend "Turn"
@ s4 legend "Chain_Separator"
8 12 32 4 12 7
12 10 33 5 10 7
16 10 32 6 10 7
20 10 32 6 10 7
# Totals 42 129 21 42 28
# SS % 0.19 0.59 0.10 0.19 0.13
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