Cannot generate restraint.gro

[Toolxx]

I am following the tutorial "https://cgmartini.nl/docs/tutorials/Martini3/ProteinsII/" and "https://cgmartini.nl/docs/tutorials/Martini3/ProteinsI/" and I found the issue that as I follow the each step, I did not generate "restraint.gro", and the "martinize2 -p" will generate nothing. It there someone meet the similar issue?

For example, I used "martinize2 -f 181L_clean.pdb -o t4l_only.top -x t4l_cg.pdb -dssp -p backbone" It only generate "
molecule_0.itp t4l_cg.pdb t4l_only.top"

How can I solve this issue? Is it from incompatible issue for python 3.8? Or some issue related to martinize2?

[csbrasnett]

Martinize2 generates position restraints within the [ position_restraints ] directive of the output itp file (unlike gmx2pdb, which writes them externally to be included).

In gmx grompp ... the -r restraint argument reads a coordinate file for position references to restrain to, using the parameters as specified in both the itp file in the [ position_restraints ] directive, and the define = ... of the mdp file.

For the purposes of the first tutorial, you can use the same position file for the initial structure and restraints, because define = -DPOSRES -DFLEXIBLE in the .mdp file only applies these to the soluble protein. You can then take a similar approach for the second tutorial too

[csbrasnett]

If anyone else is wondering about this same problem, I've expanded on my answer in the vermouth discussion forum