AMBER: how to deal with the initial structure?

From: hj zou <hjzou.iris3.simm.ac.cn>
Date: Tue, 24 Aug 2004 9:48:22 +0800

Dear amber usersúČ
       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
        



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Received on Tue Aug 24 2004 - 02:53:00 PDT
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