[gmx-users] FEP charged molecule cuestion

[Marcelino Arciniega Castro]

Hi there,

Could someone please share some ideas about the next situation?:

I am trying to estimate the relative binding affinity of two small molecules to a protein. In the setup process, ions are added in the solvent to neutralize the system. Then as everybody suggest, the ligand partial charges should be decouple to zero. But my specific case, the small molecules are charged, that means that after turning off the ligand partial charges, the system will have a net charge (because the ions in the solvent). Turning off the ions charges does not solve the problem, because of the protein charges. 

The concrete question are: 
Should I continue to atom mutation step using PME in a non-neutral system?
It would make sense to turn off the partial charges of the some atoms in the small molecule (just those that are going to be mutated)?

Thanks in advance 
Marcelino