leap adding terminal phosphates

From: Michael Cooney <mike_at_bmbiris.bmb.uga.edu>
Date: Mon 5 Mar 2001 13:20:00 -0500 (EST)

Dear Amber users:

When I load a DNA:protein complex into LEaP starting with an NMR structure
that has 5' and 3' hydroxyl termini, the program adds an incomplete
phosphate (PO2) to the 5' ends and leaves a dangling oxygen
(unprotonated) at the 3' ends. Here is an excerpt of the output:

  Added missing heavy atom: .R<DA 30084>.A<P 1>
  Added missing heavy atom: .R<DA 30084>.A<O1P 2>
  Added missing heavy atom: .R<DA 30084>.A<O2P 3>

I did not request these atoms to be added, so I wonder if there is any way
to avoid this addition and leave the OH termini as they are in the NMR

Thanks very much for any suggestions.


Michael G. Cooney
Postdoctoral Associate
Dept. of Biochemistry and Molecular Biology
The University of Georgia
Athens, GA 30602, USA
Received on Mon Mar 05 2001 - 10:20:00 PST
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