Re: [AMBER] Atom types for "alkene carbons", R.E.D.

From: case <>
Date: Fri, 29 Nov 2013 09:30:34 -0500

On Thu, Nov 28, 2013, Cecilia Lindgren wrote:
> I am trying to obtain parameters for an alkene amide bond isostere using
> the R.E.D. server. My problem is at the very end of the procedure when
> trying to choose correct atom types for the two alkene carbons.
> I am using the force field amber99SB, and when checking the available
> atom types neither one of them seem correct. It is an sp2 carbon, but it
> is not aromatic, a member of a ring or a carbonyl ... Are there no atom
> types for these carbons?

The ff99SB force field was designed for proteins and nucleic acids, not for
general organic molecules. So the list of atom types is quite limited.
You should consider using GAFF for more general molecules.


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Received on Fri Nov 29 2013 - 07:00:02 PST
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