GROMACS version: 2020.4
Hello,
I am working on a protein-ligand complex and I am performing MD simulations of this complex using the force field charmm36-jul2021. I am also using the default cgenff parameters in the force field files for ligand parametrization.
This complex has 2 ligands and the aromatic rings are well aligned in the x-ray structures. However, after starting the simulation this alignment is disrupted. How can I keep this conformation during the simulation? I think this is due to the lack of force field parameters for ligand-ligand interactions. What is the best solution for this situation?
Thanks in advance,
Berçin
