[gmx-users] Ligand breaks!

[Raj Badhan]

I'm running a simulation with a ligand and protein.
When running a EM on the ligand - protein complex, mdrun 
complains of 1-4 interactions (which I'm having a nightmare trying 
to fix) but also, when the run finishes (without converging) the 
protein is intact, but the ligand is distorted, with bonds here there 
and everywhere.
Is there any way I can freeze the ligand and run the EM with the 
ligand in the active site, but not actually including the ligand?
Cheers
Raj Badhan
Raj Badhan
Postgraduate researcher
School of Pharmacy and Pharmacetical Science
The University of Manchester
Manchester, UK.