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.
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.
- At the end of GNU file change pause -1 to set output.
- Delete line 1 to 12. The error part is at line 5, which is the setting of cbtics.
- 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.