I’m working on a project that involves using haddock to dock thousands of protein-ligand complexes on a high-performance computing cluster (the cluster uses slurm). I’m trying to generate the topology files for the ligands.
What is the best way to generate topology and other ligand parameter files locally? Because of the scale of the project, I cannot use a server or API like the ATB server, and PRODGR is down.
Thank you!