[gmx-users] how to deal with the initial structure?

[hj zou]

Dear GROMACS users,
       I'm performing a long-timescale simulation on a protein-ligand complex.And now I wanna compare the differences between apo- and holo- system.However,no crystal structure of apoprotein is available so far.So I wanna delete the ligand of holo-protein,take it as the initial structure of apoprotein and then perform a long-time simulation.Can anyone tell me whether it's reasonable or not? Any other suggestions?
      Thank you in advance.
Best regards
hjzou