How to run DSSP

User discussions
1

GROMACS version: 2018.3
GROMACS modification: NO

I have been trying to run DSSP analysis by typing: gmx do_dssp -f file.xtc -s file.tpr -o dssp.xpm -sc scount.xvg.

But I got an error saying, “ DSSP executable (/usr/global/whatif/dssp/dssp) does not exist (use setenv DSSP) ”.

How do I resolve this problem? When I was in college a few years ago, I didn’t have this problem (probably because it was the older version of Gromacs and DSSP).

2

The DSSP environment variable has to be set such that it specifies the location of the dssp binary. You’re being told that the value of $DSSP points to something that doesn’t exist.

3

Thank you for the reply.
Computing cluster person located the software for me, and I was supposed to use “mkdssp” command, instead.