Re: [AMBER] Atom type for middle nitrogen in dycyanamide?

From: David A Case <>
Date: Thu, 1 Dec 2016 13:28:09 -0500

On Thu, Dec 01, 2016, Mohd Farid Ismail wrote:
> I want to simulate an anion dycyanamide (NC-N-CN). Antechamber assigned the
> terminal N's as 'n1', and the C's as 'c1' and 'cg'. I can understand the C's
> should be 'cg', but the inner N is assigned as 'ne'. The inner N formally
> carries a negative charge, and should be sp3-hybridized. Should I accept
> this 'ne' description, or is there a better description of this nitrogen
> atom?

You should certainly treat antechamber's assignments as only suggestions,
*especially* for such an unusual bonding situation. In fact, antechamber
should probably not be used. I suggest you do a google search on "dicyanamide
force field", and you'll find a plethora of results that should be good
starting points.


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Received on Thu Dec 01 2016 - 10:30:02 PST
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