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?
the generation of topologies for novel ligands can be quite challenging (involving QM calculations & fitting of force constants/equilibrium distances/angles), and requires some in-depth knowledge about the force field that you want to apply. If you want to use the CHARMM force field a good starting point could be to generate an initial topology with the CGenFF web server. Maybe you are lucky and the obtained topology is good to go, if you need to refine/validate the parameters I recommend to take a look at the VMD-builtin ForceField toolkit or the FFParam software. Also other force fields (e.g., Amber, OPLS) have some automated programs to generate initial topologies, which may work or may not work for your ligand.