AMBER Archive (2008)

Subject: AMBER: Negative ligand

From: Syed Tarique Moin (tarisyed_at_yahoo.com)
Date: Sat Mar 15 2008 - 04:12:09 CDT

Dear all,
   
  I am trying to simulate a complex having peroxide anion (O-2)as a ligand and it is symmetrically present between the two copper +2 ions coordinated with histidines in the pdb file but after initial minimization, the peroxide anion is sligthly displaced from these two ions. I want to keep this anion as is it to know the behaviour of protein due this anionic ligand. I already calculated RESP charge of copper coordinated with histidine.
   
  Kindly suggest me
   
  Regards

       
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