Generate topolgy file using pdb and itp files

GROMACS version: 2022.4
GROMACS modification: No

Hello gromacs users, I am fairly new to gromacs and molecular dynamics. I want to simulate thiols for starters for some applications and I want to generate the topology file for thiol. I found the PDB and ITP files for sulfanyl from ATB and I tried to use ‘pdb2gmx’. I have read up on the documentation but I can’t get it to work. I am stuck on how to modify a forcefield or how to simply create a new one for the molecule. Any help on how to generate the topology would be greatly appreciated. Thanks

I am not familiar with ATB. I do not know exactly how the generated itp file looks like. It could be that you do not need the pre-processing tool gmx pdb2gmx.
In general to know more on topology files in GROMACS this manual page can be useful
Note that topology file in GROMACS are hierarchical this table on topology format can be useful
Maybe those page can help to understand file you got from ATB.

Thanks alevilla! I have progressed somewhat on the issue.