AMBER Archive (2004)

Subject: AMBER: tmd question

From: hj zou (hjzou_at_iris3.simm.ac.cn)
Date: Wed Feb 18 2004 - 20:58:45 CST


dear amber users
    Now I wanna perform a tmd simulation using amber.But I'm not sure whether it can work or not.
   I have two proteins,protein A and protein B, which form complex.The initial structure is protein A with a ligand C complexed with unbound protein B.The target structure is protein B with the ligand C complexed with unbound protein A.
   Can anyone tell me whether TMD can experience such a conformational change and provide insight into the process of conformational change?If not ,is there any other method to tackle this problem?
 Any suggestions are appreciated.

best regards
      2004-02-19

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