Re: [AMBER] Question of AM1-BCC

From: Jason Swails <>
Date: Wed, 21 Jan 2015 07:26:22 -0500

On Wed, 2015-01-21 at 11:46 +0800, asdda asa wrote:
> I am performing the parameterization of a ligand using AM1-BCC. The ligand
> contain nitrogen atom which was doubly bound to one carbon atom, singly
> bound to other nitrogen atom, and singly bound to other carbon atom, so the
> nitrogen atom has 4 valence. I noticed that the partial charge of the
> nitrogen atom was -0.013400. Is this partial charge common, I supposed
> previously that the charge for the nitrogen atom was about +1. I would be
> grateful for any comment.

This doesn't seem unusual to me. Nitrogen is slightly more
electronegative than carbon (and obviously has the same
electronegativity as itself), so I would expect it to *maybe* take more
electron density than the carbon.

Note another molecule that has nitrogen with a valence of 4 -- Lysine.
It is connected to 3 hydrogens and a carbon, and has a charge of -0.3854
in the Amber force field. The whole moiety has a net charge of +1, but
the nitrogen itself is more electronegative than its neighbors, so it
takes on a negative partial charge and the positive charges of the
neighboring hydrogens (0.34) combines to yield a net charge of +1.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Jan 21 2015 - 04:30:03 PST
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