No, I just want to make my fit more physically determined. I expect that
parameters what paramfit returns (Kp and phases) should be in agreement
with those obtained via direct FFT decomposition (because of the nature of
dihedral terms - they are the Fourier series, aren't they?). But params
returned by paramfit shows some strange and ugly results.
2017-11-15 11:08 GMT+03:00 David Cerutti <dscerutti.gmail.com>:
> 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.
>
> Dave
>
>
> On Tue, Nov 14, 2017 at 4:32 PM, viktor drobot <linux776.gmail.com> 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]
> > (SMILES)
> > 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 ambermd.org). 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
С уважением,
Дробот Виктор
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 15 2017 - 04:30:02 PST
