Re: [AMBER] Resp fiiting method and theory

From: Karl N. Kirschner <>
Date: Wed, 17 Jul 2013 10:18:29 +0200 (CEST)

Dear Carlos,

  I second Francois's suggestions for where to start looking for knowledge concerning this. I can only add my perspective and experiences.

  The MEP is computed directly from the wavefunction, and is thus an experimental observable. However, experimentally it is difficult to measure the MEP, which would allow for a comparison to the calculated one. The final optimized wavefunction, which is used to provide the MEP, is determined by the basis set and by the theory that is employed (e.g. HF, MP2, DFT).

  Alternatively, one could compare to dipole and quadrupole moments for which a wealth of experimental small molecule data exists. I have done this in a study on methanol (doi:10.1016/j.cpc.2011.05.018). I looked at how 18 different approaches for generating partial atomic charges effect the the molecule's dipole moment's magnitude and orientation, using theories ranging from OPLS charges to HF/6-31G(d) to MP2/ACCT. With certain theories, one can reproduce the experimental gas-phase dipole moment well. For example, a 0.6% error was obtained using HF/ACCD with differentiating the methyl hydrogens into trans versus guache; forcing the methyl hydrogen charges to be equivalent value (as would be needed in an MD simulation) results in an error of 17.8%. However, this resulting error is suggested to be advantageous (see the Cornell papers) for modeling systems in solution due to polarization effects.

  The end game for developing partial atomic charges and Lennard-Jones parameters, is that they reproduce some intermolecular forces dependent experimental observable (e.g. enthalpy of vaporization, diffusion rate, density). They also have some effect on the relative potential energy curve of torsion angles, which is arising from 1-4 interactions. However, in my research I have not seen this to be significant in that I believe the errors within the bonded parameters are greater in most force fields.

  If you want to check the performance of the parameters given by antechamber, with regards to reproducing QM-generated bond, angle, and torsion curves, you are welcomed to use Wolf2Pack.

Best regards,

----- Original Message -----
From: "FyD" <>
To: "AMBER Mailing List" <>
Sent: Tuesday, July 16, 2013 6:11:26 PM
Subject: Re: [AMBER] Resp fiiting method and theory

Dear Carlos T. Nieto,

I would start by:

then see:
  W.D. Cornell, P. Cieplak, C.I. Bayly & P.A. Kollman J. Am. Chem.
Soc. 1993, 115, 9620-9631. [Abstract]
  C.I. Bayly, P. Cieplak, W.D. Cornell & P.A. Kollman J. Phys. Chem.
1993, 97, 10269-10280, [Abstract]
  P. Cieplak, W.D. Cornell, C.I. Bayly & P.A. Kollman J. Comput. Chem.
1995, 16, 1357-1377. [Abstract]

Finally you might be interested in:

regards, Francois

> The question of quantum theory used and resp fitting method have been
> asked previously in the forum.
> I´m planning to obtain parameters to a series of organic molecules (no
> metal atoms) through antechamber.
> I´ve read several considerations about basis set dependence of the mep map
> obtained, but i don´t find clear the idea regarding to quantum theories,
> specially MP2, DFT and HF.
> I´ll apreciate if anyone could share their opinions about the use of this
> theories and if there is some papers that mention some comparative study.

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Received on Wed Jul 17 2013 - 01:30:04 PDT
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