AMBER Archive (2006)

Subject: Re: AMBER: RESP charge fitting for HFIP

From: Mingfeng Yang (
Date: Tue Dec 19 2006 - 01:17:24 CST

On 12/18/06, Raviprasad Aduri <> wrote:
> Hi Ming,
> First of all you need to compute the Electrostatic potential (using
> population analysis of Merz-Kollman) using QM programs such as Gaussian or

I got the molecular electrostatic potential with gamess already, using
HF/6-31G* and Merz-Kollman scheme (connolly algorithm).

Once you have the above said ESP points, you can do RESP using
> Antechamber module of Amber. I believe that you want the three Fluorines
> attached to each Carbon to be equivalent, in which case I think you want
> to
> equivalence them during the second stage of RESP charge fitting.

The problem now is the equivalencing. Usually, the methyl and methylene
atoms are optimized in the second stage. But I remember that in the Amber
mailing list, somebody mentioned Fluorine atoms should be equilvalenced in
the first stage because of its strong electronegativity.

In the input file generated automatically by RED II program, nothing is
constrained in the first stage. In the 2nd stage, the charges of CHOH atoms
are hold constant, and the 6 F atoms and the 2 C atoms in the two CF3 groups
are equivalenced, respectively. I feel this procedure is a little weird, and
guess the reverse order should be the correct choice.

Another problem is that HFIP molecule can predominately adopt two
conformations, in one of which, the H atom at the OH group can form weak
intra-molecular hydrogen bond with F atom. Shall I include this conformation
to fit the charge? According to people's experience, "Ligand coformers with
intramolecular hydrogen bonds should not considered (this was mentioned in
the original Cornell et al paper). RESP fitting of these conformers places
far too much electronegativity on the hydrogen bonding heavy atoms." I
tried to include and not include, and it seemed that the latter gave
slightly better result, but both can not generate correct charge
distribution to reproduce the liquid properties.

The results from both trials and my intuition told me that if I use a
Boltzman weight (~30% and ~70%), which approximately is the experimental
ratio of the two conformations, to include the two conformations, the
resulted charge will be perfect.

Now if my charge fitting procedure has no significant problem. Then the
choice for me is to manually fine tune the charges to reproduce the
experimental thermodynamic parameters. But this is kind of against the
philosophy behind amber force fields which always leave RESP charges alone,
and tune up other parameters, such as torsions.

My purpose is to generate a proper model maximally compatible with Amber
force field.


Best Regards
> Ravi
> At 09:44 PM 12/18/2006, you wrote:
> >Dear Amber users,
> >
> >Can anyone give some suggestions on how to fit charges for CF3CHOHCF3
> >molecule by RESP? I am not very sure about which atomic charges should
> >be equivalenced in the each of the two stages?
> >
> >Thanks,
> >Mingfeng
> >
> >
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