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

From: FyD <>
Date: Thu, 17 May 2018 12:19:32 +0200

Dear Roja,

> 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.
> 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.

Concerning using HF vs DFT computation, or generating molecular
fragments for AA, or performing chemical equivalencing for
functionalized nanotubes, I would use PyRED at RED Server Dev. at

See Tutorials:

regards, Francois

           F.-Y. Dupradeau

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Received on Thu May 17 2018 - 03:30:02 PDT
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