Generation of topology

GROMACS version: gmx, version 2020.1-Ubuntu-2020.1-1
GROMACS modification: Yes/No
Here post your question
I have been given a task to study the formation of micelles in presence of different surfactants (cationic, anionic, non-ionic etc.). For this I have drawn the each of the individual molecules in Avogadro. Now I am stuck on how to prepare the system. These are all non-standard molecules and hence in-built pdb2gmx command won’t work here. I tried the tutorial for ligand-protein binding but it has the topology of the protein generated into which the files of ligand (in form of itp as generated by cgenff and then converted to gmx format by the python script). But here I do not have any such protein molecule. How can prepare the system here?

Hi,
The next step is decided which force field you want to use to describe your systems (based on the parameters availability). Then you can check if there are any tools (e.i see Third party tools and files - GROMACS forums) that can generate GROMACS topology files.
or follow what previous was suggested
Setting up gromacs for the first time

Best regards
Alessandra