AMBER Archive (2009)

Subject: [AMBER] FE: unexpected coordination 4 - using nonstandard tree type '4'

From: ben rodriguez (bramber_at_live.com)
Date: Fri May 15 2009 - 17:09:44 CDT


Hi all, I am triyng to run dynamics on a deoxy heme protein using a heme-his residue. When building the topology file I get the following message about the Fe coordination. Can anyone explain what this message means, and if this is appropriate for deoxy heme simulations. I am using ff99SB.

Thanks,
Ben

  (FE: unexpected coordination 4 - using nonstandard tree type '4')
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

    res total affected

    CGLY 1
    NMET 1
    WAT 4814
  )
 (no restraints)

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