Covalent docked system MD analysis

I have performed screening of some molecules and also carried out Covalent docking studies. Now I want to perform MD analysis of the complexes which are showing good covalent interactions. Can I start with covalently formed complex of ligand-receptor as starting point of MD or do I need to use non-covalent complex?

If I have to start MD with non-covalent complex, then how should I analyze the results / output from MD?


It depens in what you are interested in a covalently bonded ligand or non covalently bonded ? If you are interested in a system where the ligand is covalently bonded, then you simulate the ligand covalently bonded and all the bonded intereactions between the ligand and the acceptor have to properly defined in the topology file.

Best regards