I am also facing problem to dssp3 and dssp2.

some tool recommended dssp2 but conda provide dssp3.

Hi

https://manual.gromacs.org/current/install-guide/index.html

I have a copy of the binary for dssp 2.0.4 on my Github (I have used this to coarse-grain proteins to Martini 2 ff using martinize.py) -

https://github.com/DJ004/MolDynamics_gromacs/blob/main/dssp/dssp-2.0.4-linux-i386

To run martinize.py :

python2 martinize.py -f all_atom_protein.pdb -x protein_cg.pdb -o topol.top -dssp dssp-2.0.4-linux-i386 -ff martini22 -elastic -ef 500 -el 0.5 -eu 0.9 -ea 0 -ep 0

To coarse-grain using martinize2 (https://arxiv.org/pdf/2212.01191.pdf), you need dssp 3.0.0. Create a conda env, "pip install vermouth" to install martinize2, and then "conda install -c salilab dssp" to install dssp 3.0.0. "which mkdssp" will give you the path to the (mk)dssp 3.0.0 executable.

To run martinize2 :

conda activate martinize2_vermouth # activate conda env

martinize2 -f all_atom_protein.pdb -x protein_cg.pdb -o topol.top -elastic -dssp ~/miniconda3/envs/martinize2_vermouth/bin/mkdssp

Hi