Re: QMMM Question

From: Brian Radak (brian.radak_at_gmail.com)
Date: Thu Feb 14 2019 - 13:04:50 CST

Hi Kelly,

In general, I don't think there is a high opinion of minimal basis
semi-empirical methods for modeling multivalent ions in biological systems.
A d-orbital augmented method (e.g. MNDO/d or AM1/d) *might* do ok, but the
parameters probably don't exist and you would likely end up calibrating to
WFT/DFT. Personally, I would benchmark PM7 (or whatever) in this fashion
anyway, probably looking at ligand exchange energies, otherwise you risk a
harsh dismissal by a journal referee.

Cheers,
BKR

P.S. The QM/MM implementation in NAMD may also have trouble with highly
charged quantum regions due to the way long-range electrostatics are
handled. The ligands that coordinate your ion might matter a lot.

On Thu, Feb 14, 2019 at 12:28 PM McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> I am trying to get binding energies and heats of formation of a divalent
> copper binding to 4 sidechains in a protein. I have been doing QM/MM
> using PM7, but I'd like to get some opinions from more experienced
> computational biophysicists/chemists. For something like divalent copper,
> is it really worth treating my QM region with PM7? What results/values can
> I really trust from this? Or do you recommend a higher theory, like DFT,
> to apply to my QM region, even though that would slow down the computation
> significantly, but give better results?
>
>
> *Kelly L. McGuire*
>
> *PhD Candidate*
>
> *Biophysics*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
>

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