DSSP analysis in AMBERTOOLS

DSSP refers to Dictionary of Secondary Structures of Proteins. It’s a rough method to analyze protein secondary structures along with time in MD simulations.

The following is an example. Cited from http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water_(Pt._2)

There are many softwares or MD simulation package can do such an analysis. I prefer to use AMBERTOOLS.

The script is below.

parm test.prmtop
trajin test.mdcrd
secstruct :1-100 out dssp.gnu

The GNU file has some problem and you can not get a picture from it.

I did the following modification to generate PNG file or PDF file.

  1. At the end of GNU file change pause -1 to set output.
  2. Delete line 1 to 12. The error part is at line 5, which is the setting of cbtics.
  3. Change line 13 splot “-” with pm3d title “dssp.gnu” to splot “-” u ($1/10):2:3 w pm3d title “dssp.gnu”. You may change $1/10 according to your relationship between frame and time.

The head of GNU file can be changed to the following content. 

reset
unset key
set grid
set terminal pngcairo
set size 0.96,1
set encoding iso_8859_1
set xtics nomirror
set ytics nomirror
set pm3d map corners2color c1
set cbrange [  -0.500:   7.500]
set cbtics    0.000,1,7
set palette maxcolors 8
set palette defined (0 "white",1 "#0000FF",4 "#00FF00", 5 "grey", 7 "#FF0000")
set cbtics("None"    0.000,"Para"    1.000,"Anti"    2.000,"3-10"    3.000,"Alpha"    4.000,"Pi"    5.000,"Turn"    6.000,"Bend"    7.000)
set xlabel "Time (ns)"
set ylabel "Residue Number"
set yrange [   0.000: 600]
set xrange [   0.000: 84]
set title "DSSP of this protein"
set output "dssp.png"
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