GROMACS version:2025.2
GROMACS modification: No
Hi. I’m new to GROMACS. I am working on a protein ligand complex simulation. I generated topology file for the protein ATIII that I’m working but had doubt about how to generate topology for the ligand. I tried following the tutorial available on mdtutorial but my faculty-mentor suggested to generate topology in a different way since the ligand I’m using is non–standard.
So, I wanted to ask how to generate generate topology file for a non-standard ligand file?