[gmx-users] free energy perturbation

[antonio]

Dear gromacs users
I am trying to carry out a free energy perturbation to evaluate the
difference in binding energy between two inhibitors of the same protein.
I have read a lot of post but i did no understand how to create the
topology file.
have i to write a mixed pdb of the two inhibitors structure modifying
the value of beta factor to -1;0,1 for disappearing and rising atoms and
than to proceed by pdb2gmx ?
Could someone please link a tutorial or a guide to follow.
thanks in advance
Antonio