I have performed covalent docking using maestro and want to convert the files to gromacs and then perform covalent md simulation.
I have been able to run the non covalent md simulation but not been able to retain the covalent bond while making gromacs file. Please help regarding this.
That is a visual artifact. For example, VMD guesses where the bonds are based on the inter-atomic distances. So what you are seeing here is the H attached to the S on the left is bent over towards the right S. And it is close enough such that VMD thinks they should be bonded.
Check your topology around the left S and it’s H, something is probably missing.