AMBER Archive (2009)

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

From: case (
Date: Wed Sep 02 2009 - 21:15:14 CDT

On Wed, Sep 02, 2009, Lin Xu wrote:

> 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?

I'm not sure why you think rotation should be rare. Torsional barriers
for aromatic nitro groups seem to be quite variable in quantum chemistry
calculations (depending on the other substituents on the ring), but are
often predicted to be quite low.

However, this variability means that antechamber has to make some real
guesses. You should treat what antechamber produces as a (good?) first guess.
You are encouraged to conduct your own investigation of what the torsional
barrier "should" be, then adjust the antechamber force constants to provide a

...good luck...dac

AMBER mailing list