[gmx-users] do_dssp normalization error

[loan.huynh at utoronto.ca]

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