AMBER Archive (2004)

Subject: AMBER: how to deal with the initial structure?

From: hj zou (hjzou_at_iris3.simm.ac.cn)
Date: Mon Aug 23 2004 - 20:48:22 CDT

Dear amber 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
        

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu