Re: [AMBER] RESP fitting in solvent

From: FyD via AMBER <>
Date: Tue, 28 Nov 2023 18:35:55 +0100

Dear Jakub,

> I have a question about the RESP fitting procedure. I am simulating a
> cis-platin derivative and therefore, I am using a module to
> parametrize
> it. Throughout the whole process, that is the geometry optimization and force
> constant calculation, I have employed a B3LYP functional with TZVPP base with
> CPCM water as a solvent.

For optimizing the geometry of a molecule with a transition metal,
using DFT makes sense...

For transition metal complexes you may find more accurate DFT
computations (than B3LYP) in literature:
     such as M06, WB97XD, others? (I like WB97XD for transition metal,
hydrogen bond)

Using an implicit solvation model during geometry optimization is up to you:
You could easily study the impact of this implicit solvation model
during geometry optimization by running computations with versus
without this solvation model. Using Water as a solvation model means
you observe key interactions in water you want to favor (or prevent)...

> However, when it comes to ESP calculation, I am unsure what to do. I have
> understood that because of error calculation, standard RESP fitting
> in Amber is
> done on a HF/6-31G* level in vacuum.

For organic molecules yes.

> Because I have a Pt atom in my compound, I
> have to employ a bigger bases set, so I decided to stick with the
> level I have
> used for optimization and frequency calculation, B3LYP/TZVPP.

For bioinorganic complexes DFT is also generally used in MEP computation...

> My question is,
> should I include a CPCM solvent in the ESP calculations as well ?

Why do you want to use this implicit solvation model?

For instance if you read the work of Duan et al. (AMBERFF03; the authors used an
implicit solvation model to mimick the interior of proteins...

> I have
> already performed both of the RESP fitting, without solvent and with the
> solvent and the charges are quite different.

Well comparing charge values is complex...

> Which of them should I use im
> subsequent MD simulations ?

Again why do you want to use a water implicit solvation model? - no
need to asnwer ;-)

if you have a good reason for using a water implicit solvation model
in MEP computation, you could compare the impact of using it versus
not using it during MD simulation...

You could also use R.E.D. Server Dev./PyRED to generate your force
field for transition metal complexes...

I hope this helps
Best Francois

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Received on Thu Nov 30 2023 - 12:00:02 PST
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