I am working on aggreagte of small organic molecule and have generated force field parameters using AMBER. However, when I perform a standalone QM/MM calculation using the Janus model in Q-Chem, the molecular structure breaks during the optimization of qm molecule and new bonds are formed that do not exist in the original molecule.
Has anyone encountered a similar issue or can suggest what I might be missing? I would appreciate any advice regarding possible problems with the force field conversion, topology definition, atom typing, bonded parameters, or the Janus setup in Q-Chem.
Thank you for your help.