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

From: roja rahmani <>
Date: Fri, 18 May 2018 17:03:26 +0430

On Fri, 18 May 2018, 16:40 David A Case, <> wrote:

> 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.
Sorryyy, i couldn't understand you.
My nanotube is ZnS which is better to optimize by DFT.
All in all you think it is not true to use DFT calculation for amino acid
partial charges?

> (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.)
Yes, but i should compare my results to the prior results and system(with a
little changing) which i calculated them by AMBER99. So if i change the ff
i think the "comparison" is not valuable and rational to be published.
This is my idea but I don't know this scrupulosity is needed or not. What
do you think as you are experienced?

> ....dac
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Received on Fri May 18 2018 - 06:00:05 PDT
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