- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: viktor drobot <linux776.gmail.com>

Date: Wed, 15 Nov 2017 15:14:55 +0300

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
*

*>
*

Date: Wed, 15 Nov 2017 15:14:55 +0300

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>:

-- С уважением, Дробот Виктор _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Nov 15 2017 - 04:30:02 PST

Custom Search