Re: [AMBER] charge fitting procedure in amber

From: Karl Kirschner <>
Date: Tue, 15 Dec 2015 09:16:51 +0100

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

  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.


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* RESP
> 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
> _______________________________________________
> AMBER mailing list

Karl. N. Kirschner, Ph.D.
Research Associate
Bonn-Rhein-Sieg University of Applied Sciences
Grantham-Allee 20, 54757 Sankt Augustin, Germany
AMBER mailing list
Received on Tue Dec 15 2015 - 00:30:03 PST
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