I used the Charmm GUI for Adenosylcobalmin B12 topology generation. It removes the cobalt atom from the molecule. Can you please suggest how can this fixed or another solution for generating the topology of this molecule
The CHARMM force field does not (officially) support cobalt, though there are parameters in the literature that could be used. This would require manually preparing the system as CHARMM-GUI is not capable of doing it.