In the pmx tutorial, it is described a workflow for thermodynamic integration of ligand. For the generation of the double topologies a gromacs file *.itp is required: is there a way to write it? I previously parametrized my system with tleap in order to use Amber force field. So my gromacs topology file has all the solute atoms in a single group since I used the Acpype parser to obtain input file for MD simulations. Do I have to select by hand all the ligand parameters or is there a simpler way?
Thanks for the help