On Wed, 21 Sep 2016 12:00:29 +0000
Abdülkadir KOÇAK <ko...@gtu.edu.tr> wrote:

> In terms of endstates, the state A is the real ligand complexed with
> Protein in water... I did not define dummy atoms for the ligand as
> the state B, which I believe I should have...

I'm not quite sure what you mean here.  I think any recent Gromacs
version (maybe from 4.x?) allows you to use the couple-* parameters in
the mdp file.  In this way you do not need a modified topology.  On the
contrary, you would use a topology just as for standard MD simulation.
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