AMBER Archive (2004)

Subject: AMBER: Nitrogen vdw type

From: Terry Downing (terry_at_francisco.compbio.ucsf.edu)
Date: Tue Feb 10 2004 - 16:56:37 CST

 Hey Everyone,

   In my research involving RNA, I have noticed that for both Amber and
 OPLS, there appears to only be one VDW radius and well depth for
 nitrogen regardless of chemical environment. For example, both amino
 nitrogens and aromatic nitrogens have the same radius and well depth.
 Is this true or am I missing something? If I am correct, what were the

 original experiments that supported this decision? Has there been any
 follow-up work in this area? Any information about this would be
 appreciated. Thanks in advance for you help.

 Sincerely,
Terry Downing

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