What is the good version of [DSSP tool] to be used by 'gmx do_dssp'?

GROMACS version: 2021.1
GROMACS modification: No


I want to use the gmx do_dssp command (e.g., I tested: gmx do_dssp -f md_300ps.xtc -s md_300ps.tpr -o dssp_test.xpm) but it gave the errors below:
Program: gmx do_dssp, version 2021.1
Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 603)

Fatal error:
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)

In fact, in my HPC, we installed the dssp 3.0.0 from anaconda: https://anaconda.org/salilab/dssp

I tested the command using this: It works as below

$ mkdssp
mkdssp 3.0.0 options:
-h [ --help ] Display help message
-i [ --input ] arg Input PDB file (.pdb) or mmCIF file (.cif/.mcif),
optionally compressed by gzip (.gz) or bzip2 (.bz2)
-o [ --output ] arg Output file, optionally compressed by gzip (.gz) or
bzip2 (.bz2). Use ‘stdout’ to output to screen
-v [ --verbose ] Verbose output
–version Print version and citation info
-d [ --debug ] arg Debug level (for even more verbose output)


To calculate the secondary structure for the file 1crn.pdb and
write the result to a file called 1crn.dssp, you type:

mkdssp -i 1crn.pdb -o 1crn.dssp

What is the good way to make GROMACS ok to use ‘mkdssp’ or I must install dssp version 2 from https://anaconda.org/speleo3/dssp?

Also, does GROMACS use ‘mkdssp’ or ‘dssp’ command when calling the DSSP tool?

Thanks for your help.


export DSSP=mkdssp

Hi @liuyujie714 Thanks so much. It works.