Error during EM

Hey everyone!
I am running a simulation with a complexe of a protein and a ligand whose input files are prepared by CGennFF server.I have got this error in EM step:

it stops in 15th step. As I surfed the internet, I found there might be a problem in ligand topology file. however, I don’t have any idea how to fix this.


This might be due to a few atoms being very close to one another - energy minimisation would attempt to move a few of them along an energy gradient, but in a scenario with lots of interactions end up placing them on top of another.

I suggest you have a look at atom 7932. Another option you could try is decreasing the initial step–size for the energy minimisation.

Infinite energy usually means unrealistic coordinates. I doubt the problem is the topology itself but complete details of troubleshooting protein-ligand complexes are given at

thank you all.