Re: [AMBER] charge fitting procedure in amber

From: Karl Kirschner <>
Date: Tue, 15 Dec 2015 11:16:13 +0100

Hi again,

  One more thing to note. In my opinion, the Amber manual's statement,
"However, in most cases, AM1-BCC, which was parametrized to reproduce
HF/6-31G* RESP charges..." is not entirely true (but it does capture the
general conclusion). The two AM1-BCC papers [1,2] state that this method
was developed to reproduce HF/6-31G(d) electrostatic potentials, which is
the same QM theory used in the HF/6-31G* RESP charges that are present
within the AMBER residue database (i.e. all proteins and DNA residues).
However, the QM electrostatic potentials that were used as fitting targets
were created in a very slightly different manner and then compared to RESP
charges using different scaling factors (i.e. 0.001/0.01 [2] versus
0.0005/0.001 [3]). Never-the-less, the take-home-message seems to be that
the two charges sets generally have similar partial atomic charges.


1.Jakalian, A.; Bush, B. L.; Jack, D. B. & Bayly, C. I. Fast, efficient
generation of high-quality atomic charges. AM1-BCC model: I. Method Journal
of Computational Chemistry, John Wiley & Sons, Inc., 2000, 21, 132-146
2. Jakalian, A.; Jack, D. B. & Bayly, C. I. Fast, efficient generation of
high-quality atomic charges. AM1-BCC model: II. Parameterization and
validation Journal of Computational Chemistry, 2002, 23, 1623-1641
3. Bayly, C. I.; Cieplak, P.; Cornell, W. & Kollman, P. A. A well-behaved
electrostatic potential based method using charge restraints for deriving
atomic charges: the RESP model The Journal of Physical Chemistry, 1993, 97,

On Tue, Dec 15, 2015 at 9:16 AM, Karl Kirschner <>

> Hi Conor,
> In my opinion it is something that you need to worry about, but just a
> bit. The AM1-BCC charges do tend to be similar to those determined by
> HF/6-31G(d) RESP Connolly method, but they are not identical. For your
> system, I would advise creating several models using different charge sets
> and different water models. I am not aware of a study where someone has
> determined the water model that is best suited from simulating crystal
> growth. By performing simulations on several different models, you can look
> for common trends between them. It would even be better if you have an
> experimental observable(s) that could be used to validate a particular
> model.
> I assume that the Gaussian input file problem that you are having is for
> computations on a single molecule. Unless you are trying to account for
> polarization effects some how, most RESP calculations are done on single
> molecules (i.e. not a single input file containing glycine-methanol-water).
> If the glycine is a zwitterion, you might have some problems performing the
> quantum gas-phase optimizations. The use of a rigorous theory and a large
> basis set will lead to a proton transferring from the nitrogen to the
> carboxylate group. By using a small basis set (at least with HF theory) you
> can obtain a charge separated species in the gas phase. I am not sure what
> AM1 will do with a glycine zwitterion.
> Hope that helps some.
> Bests,
> Karl
> P.S. You might be interested in looking at our paper on zweiterion force
> fields (DOI: 10.1002/jcc.10174). In that paper there are references to
> some experimental data for glycine and to articles that see the proton
> migration in QM calculations.
> On Mon, Dec 14, 2015 at 10:27 PM, conor parks <>
> wrote:
>> Hello everyone,
>> I was wondering if someone could help me understand which charge fitting
>> procedure is appropriate for my case. I am trying to find the GAFF force
>> field parameters for methanol using tutorials (
>> I am planning to
>> perform a
>> glycine methanol water crystal growth simulation. I am not sure if it is
>> ok
>> for me to use the BCC charge fitting scheme vs. RESP. The majority of the
>> tutorials I have found online use the BCC fitting procedure, and the
>> manual
>> states the following, making me think the BCC and RESP methods should
>> yield
>> equivalent physics:
>> The charge methods used in GAFF can be HF/6-31G* RESP or AM1-BCC.[285,
>> 286]
>> All of the force field parametrization were carried out with HF/6-31G*
>> charges. However, in most cases, AM1-BCC, which was parametrized to
>> reproduce HF/6-31G* RESP charges, is recommended in large-scale
>> calculations because of its efficiency.
>> Could someone help guide me into determining whether this is something I
>> need to worry about? I have been trying to generate the charges using
>> RESP,
>> but have been having issues generating the gaussian input file.
>> Regards,
>> Conor Parks
>> B.S.E in Chemical Engineering, University of Michigan, 2012
>> PhD candidate in Chemical Engineering, Purdue University
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Received on Tue Dec 15 2015 - 02:30:04 PST
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