Re: [AMBER] Question in Amber atom types

From: David A Case <>
Date: Wed, 21 Jan 2015 21:13:10 -0500

On Thu, Jan 22, 2015, asdda asa wrote:
> I am using amber force field (GAFF) to parameterize a ligand. The ligand
> contain two same moieties attached to different positions. However, the
> atom types of each atom of the two moiety is not exactly same. There is one
> same carbon atom having different atom type, one carbon is assigned as cd,
> while the other carbon atom was assigned as cc. How can these two
> different. The two carbon is exactly same.

The atom types cc and cd are mirrors of each other, and will give identical
behavior. This is discussed at some length (see the discussion related
to Table 1) in the original GAFF paper (J Comput Chem 25: 1157, 2004).


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Received on Wed Jan 21 2015 - 18:30:02 PST
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