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

From: FyD <>
Date: Fri, 29 Nov 2013 17:50:54 +0100

Quoting case <>:

>> 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.

I think there is no problem in this case...

regards, Francois

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Received on Fri Nov 29 2013 - 09:00:02 PST
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