How to use mkdssp

GROMACS version: 2018.3
GROMACS modification: No

I want to check secondary structure of a protein throughout the simulation time, using mkdssp
(mkdssp -i input.pdb -o output.dssp)

Q. Can anyone tell me how to convert an output file from NPT production (cpt, edr, gro, xtc) into a PDB file?
Q. Also, how do I open a .dssp file?

I am rather more familiar with do_dssp than mkdssp.

Thank you.

do_dssp is just a wrapper that calls dssp, mkdssp, xssp, or whatever_they_call_it_now. You don’t invoke the DSSP program manually to analyze a trajectory. $DSSP needs to point to the (in your case) mkdssp binary and you should do the analysis with do_dssp.

gmx editconf -f input.gro -o output.pdb

But again, you don’t need to do this for the analysis you’re seeking to perform.

Thank you for the reply.

In the working directory, I typed which mkdssp.
Then I copied the path after export DSSP=, and it worked.

Thank you for your help.