Re: [AMBER] wrong geometry amide nitrogen

From: Junmei Wang <>
Date: Tue, 28 Apr 2020 17:02:10 -0400

Gaff adopted the good parameters from amber biomolecular force field. So
the peptide-like parameters should be similar. For you minimization, did
you consider solvent effect? If you send me your prep file, I will check if
it is a force field issue or not.



On Fri, Apr 24, 2020 at 11:02 AM David A Case <>

> 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 Tue Apr 28 2020 - 14:30:02 PDT
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