AMBER Archive (2009)

Subject: [AMBER] how to deal with aromatic nitro group with antechamber

From: Lin Xu (linxu_at_stanford.edu)
Date: Wed Sep 02 2009 - 17:04:13 CDT

Hello,
I have been trying to generate residule topology file for an enzyme inhibitor (38 atoms) using antechamebr. My molecule contains an aromatic nitro group. I used Amber10, AM1-bcc charge and gaff atom type. The atom type for nitro nitrogen assigned by antechamber was "no (N in nitro group)". However, in my simulation, the nitro is rotating vigorously. Considering it is conjugated to a benzene ring, the rotation of nitro should be very rare. I am wondering if there is any special way to deal with aromatic nitro groups?
Thanks in advance!
Lin

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