Re: [AMBER] wrong geometry amide nitrogen

From: David A Case <>
Date: Fri, 24 Apr 2020 11:01:49 -0400

On Fri, Apr 24, 2020, Arnaud Bondon wrote:

>). Clearly the N10 amide nitrogen
>has an pyramidal character. And the omega dihedral angles are not good
>The molecule was prepared as a mol2 file Nitrogen are

The input atoms types don't matter: you should look at the output types
in the prep file. If this is a peptide-like molecule, it may be that
the gaff types don't do as well as the tuned Amber atom types.
You might want to see what happens if you request Amber atom types.

I'm not sure whether GAFF has types that are specifically tuned for
peptide bonds or Junmei here.

...good luck...dac

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Received on Fri Apr 24 2020 - 08:30:02 PDT
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