AMBER: Negative ligand

From: Syed Tarique Moin <>
Date: Sat, 15 Mar 2008 02:12:09 -0700 (PDT)

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

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Received on Sun Mar 16 2008 - 06:07:52 PDT
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