AMBER: nonplanarity of NH2 groups

From: laura zanet <>
Date: Wed, 6 Dec 2006 07:48:33 -0800 (PST)

Dear all,
  My question is about NH2 non-planarity. If I carry out AMBER minimizations on nucleic acids, what kind of non-planarities can I expect? For example, is it normal to get a value of 10 degrees for the N3-C4-N4-H41 dihedral in cytosine? I know the AMBER force feild cannot model this type of non-planarities, but I want to know if deviations from planarity of 10-15 degrees are normal.
  I hope you can help me.

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Received on Fri Dec 08 2006 - 16:23:00 PST
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