I have noticed that FEP calculations are now supported for membrane proteins! This is great news and I would like to thank the community for their efforts.
I am now trying to use the FEP tool to compare free energy of binding of Na and Li ions in the binding site of a transmembrane protein, and I would appreciate your guidance in setting this up. I already have a snapshot from MD simulations in which Na ion is bound in the binding site. So I would like to perform FEP on this ion and then would like to place Li ion in the same site and repeat the FEP calculation.
I have created a pdb of the protein/Na complex (with Na ion designated at HETATOM). It seemed that Na was designated as the ligand throughout the system build up, but at the last stage, when mol2 format file was generated, there was an issue with force field generator and I don't know how to fix the problem.
Can you please let me know what can be done?