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.
-SARA
Hi,
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 http://manual.gromacs.org/current/user-guide/terminology.html#diagnosing-an-unstable-system
thank you all.
