[gmx-users] typeB in FEP calculations

[Rui Neves]

Hi Gromacs users,

I am trying to determine a relative binding free-energy of two hypothetical
ligands (A -> B).

To do this, I must indicate a typeB for the atomtypes in B.
Once this is done, do I have to explicitly include the bonded parameters
for the B state, if I started by loading all the parameters of the force
field that parameterizes both ligands?

Thank you for any help,

Regards,

Rui Neves