Re: [AMBER] DFT method for calculating amino acids partial charges in AMBER99

From: David A Case <>
Date: Fri, 18 May 2018 08:10:07 -0400

On Thu, May 17, 2018, roja rahmani wrote:
> I want to calculate partial charges for nanotube capped with amino acid. I
> use DFT calculation when it is just nano tube with out any amino acid. As
> far as i know the amino acid partial charges for AA in amber99 are
> calculated by HF/6-31G* RESP calculation.

This is correct.

> If i use DFT calculation for optimizing and calculating partial charges for
> nanotube- amino acid system, would amino acid partial charges be wrong or
> overstimated? I want to use this structures an an input for MD simulations
> in GROMACS using amber99 ff.

DFT charges would not be "over-polarized" to the same extent as HF
charges, and so would not be consistent with the partial charges used in
force fields in the "Cornell et al." family, of which the current
version is ff14SB.

Depending on the composition of your nanotube, this might or might not
make much difference.

(I can't help repeating, if only for the benefit of other readers of the
list: we strongly recommend against using the amber99 force field for
peptides or proteins.)


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Received on Fri May 18 2018 - 05:30:04 PDT
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