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

hj zou hjzou at iris3.simm.ac.cn
Tue Aug 24 03:45:51 CEST 2004

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

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