@jalemkul Thanks in advance for your always support. This problem has a simple solution, as explained below:
1- First, the user should install DSSP using a Linux terminal:
sudo apt-get update
sudo apt-get install dssp
2- Change mkdssp to DSSP using the following command:
sudo ln -s /usr/bin/mkdssp /usr/local/bin/dssp
3- Next, run the below command to get the results. The user should not forget to add [-ver 4] flag when she/he runs the gmx do_dssp command. It works fine, and immediately, gromacs calculates the results for this command.
gmx do_dssp -ver 4 -s md.tpr -f md.trr -o ss.xpm -sc scount.xvg
4- You can convert *.xpm file to jpg or png using following commands:
mogrify -format jpg *.xpm (for jpg output)
or
mogrify -format png *.xpm )for png output)
5- Now, you can use the generated plot for your publication.
