AMBER Archive (2006)

Subject: AMBER: nonplanarity of NH2 groups

From: laura zanet (laura.zanet_at_yahoo.com)
Date: Wed Dec 06 2006 - 09:48:33 CST

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.
  Thanks,
  Laura

 
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