[gmx-users] content of secondary structure output file

ahmet yıldırım ahmedo047 at gmail.com
Mon Sep 24 09:31:30 CEST 2012


Dear users,

I am using the command as the following.
A part of output file (secondary-structure.xvg) is as follows.
1.column: time
2.column:structure
3.column:coil
...
I do not understand the meaning of 2.column.
What is "structure"? What is the meaning of value there?

Greetings

secondary-structure.xvg:

# This file was created Mon Sep 24 09:55:49 2012
# by the following command:
# do_dssp -s protein-RUN.tpr -f traj-nojump.xtc -o secondary-structure.xpm
-sc secondary-structure.xvg
#
# do_dssp is part of G R O M A C S:
#
# Grunge ROck MAChoS
#
@    title "Secondary Structure"
@    xaxis  label "Time (ps)"
@    yaxis  label "Number of Residues"
@TYPE xy
@ subtitle "Structure = A-Helix + B-Sheet + B-Bridge + 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 "B-Sheet"
@ s3 legend "B-Bridge"
@ s4 legend "Bend"
@ s5 legend "Turn"
@ s6 legend "A-Helix"
@ s7 legend "5-Helix"
@ s8 legend "3-Helix"
@ s9 legend "Chain_Separator"
       0   341    74   131     4    43    38   168     0     0     1
      20   331    84   119     6    37    41   165     0     6     1
      40   333    78   121     8    41    39   165     0     6     1
...
-- 
Ahmet Yıldırım



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