Re: [AMBER] The strange way of paramfit working process

From: David Cerutti <>
Date: Wed, 15 Nov 2017 03:08:10 -0500

If I understand correctly, you are trying to circumvent what paramfit was
telling you. Paramfit stipulates that the parameters it fits must bridge
the gap between the molecular mechanics energies it knows and the quantum
energy profile of the system. I don't fully understand your alternative
procedure, but Paramfit did take into account the 1:4 interactions and any
other terms as it fit the dihedral force constants. So, take the results
from paramfit--that frcmod is producing a reliable model. You can also use
the mdgx program to accomplish this--it will produce tighter fits, ceteris
paribus, and a rich description of how the parameters it optimized operate
in the training set--but the mechanism of each code is essentially the same.


On Tue, Nov 14, 2017 at 4:32 PM, viktor drobot <> wrote:

> Hello community!
> We are working on parameterizing of some molecule (6-aminopenicillanic
> acid) and for these moment we are trying to find right dihedral terms for
> hydrogens attached to nitrogen (we're rotating NH2 group). Because of
> tricky nature of the 6-APA we're decided to 'decompose' molecule to set of
> smaller fragments. One of these molecules: C1(C(=O)N(C1=O)[H])N([H])[H]
> After geomeptry optimization in Gaussian and RESP charge fitting we rotated
> the NH2 group around N-C bond with stepping of 5.0 degrees (full circle)
> and conducted single-point energies run at Gaussian (according to the
> "paramfit" manual at So we have potential energy profile for
> NH2 rotating.
> As we understand it these energy profile contains not only dihedral
> interactions of hydrogens on amino group but also van der Waals and
> electrostatics with other atoms in molecule. We assigned basic parameters
> from GAFF field with parmchk2 and decided to fit energy term for H-N-C-C
> dihedral but not with plain paramfit.
> As soon as we know the Amber energy is: E = bonds + angles + dihedrals +
> vdw + el
> So for the first step we set Kp value for H-N-C-C dihedral term to 0 (in
> hope that in result we obtain all energy terms with these one excepted: E =
> bonds + angles + dihedrals* + vdw + el). For the sake of simplicity we're
> conducted dummy fit of the K value with paramfit and get MM energies from
> the output file (WRITE_ENERGY is set in job control file). After that we
> subtracted these energies (blue line) from quantum data (orange line) in
> hope that now we will have pure dihedral energy dependency on the angle of
> NH2 rotation (yellow line). All these dependencies are on attached plot
> [image: Встроенное изображение 2]
> ​
> As soon as we obtained pure dihedral energy profile we conducted the FFT
> transform on these data and obtained Fourier coefficients and phase shifts.
> We are decided to get the first 4 harmonics of Fourier series (because of
> high amplitude density) and discarded null coefficient because it's only
> matter of fitting the K value soon:
> Np Kp Phase
> 1 1.06514231 -111.231865
> 2 0.32663696 137.269480
> 3 0.13145744 7.266503
> 4 0.08701518 -77.208482
> Then we constructed energy profile back with this formula:
> E(phi) = Kp_1 * (1 + cos(phi + phase_1)) + Kp_2 * (1 + cos(2 * phi +
> phase_2)) + Kp_3 * (1 + cos(3 * phi + phase_3) + Kp_4 * (1 + cos(4 * phi +
> phase_4))
> The result is shown on the image above (green line; compare with the yellow
> line - only vertical shift is needed...). Seems like the results obtained
> are in good agreement with our assumptions (brown line; compare with the
> orange one). For the frcmod file we're inverting signs of phases (as soon
> as Amber requires E(phi) = Vn * (1 + cos(n * phi - gamma_n)))
> After that we edited frcmod again and now replaced old term for H-N-C-C
> dihedral with four new with parameters from FFT analysis. But next things
> went bad. After fitting the K value we can't get right energy profile as
> brown line on above plot! Things are messed up[image: Встроенное
> изображение 3]
> We are supposing that paramfit needs some transformed angles on its input
> or we are need to apply shift to our phases (already tried pi, -pi and sign
> inversion). Other thoughts that some mess are on the stage of getting pure
> dihedral energies...
> Can you help us? We're completely stuck upon it. Blind fit of phases and/or
> Kp's in paramfit gives us physically non-sense values so we want to do that
> on concrete basis. Thank you!
> --
> С уважением,
> Дробот Виктор
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Received on Wed Nov 15 2017 - 00:30:02 PST
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