Thank you all! I will try pure paramfit and mdgx too.
Physical nonsense values for me is when Kp parameters are negative values.
And why you set phases strict to 0 or 180? Can't there be negative or
non-int phases?
2017-11-17 3:42 GMT+03:00 David Cerutti <dscerutti.gmail.com>:
> Hi Viktor,
>
> Sorry I can't seem to be of much help, either--the dihedrals are a Fourier
> series but I've never heard of fitting them by doing a Fourier transform.
> Simple enough to do the least squares optimization of each coefficient. If
> you want to try out mdgx, it should be able to work with your structures
> and input energies, then produce parameters. I did a lot of work to try
> and make it user-friendly, let you explore what new parameters you want to
> add, but it's still not a walk in the park. I helped another group awhile
> back and while I appreciate their tenacity and interest in the project, it
> reinforced my belief that force field development takes as long as you are
> willing to give it.
>
> I will continue to try and improve mdgx and the Amber modeling process, but
> there are so many different opinions on how to proceed, each of which is
> deep-seated and not necessarily compatible with the others. The modeling
> programs tend to reflect the opinions of the people who wrote them. I will
> suggest that a broader goal of force field development should be higher
> fidelity to the quantum benchmarks so that better quantum benchmarks can
> shine through the noise that our crude approximations inject. Without a
> guiding light and without better molecular mechanics approximations, fights
> over our personal opinions are all that we're going to get over the
> meanings of those shadows on the wall of the cave.
>
> Dave
>
>
> On Thu, Nov 16, 2017 at 7:26 PM, Robin Betz <robin.robinbetz.com> wrote:
>
> > Hi Viktor,
> >
> > Paramfit's energies are all calculated using the full AMBER equation, and
> > do not represent the pure dihedral energy profile.
> > If you want to fit to this sort of profile only, your fitting procedure
> > generates a frcmod suitable for further use. Like you mention though,
> > quantum calculations do incorporate nonbonded and other bonded
> > contributions to the total energy.
> >
> > What do you mean by physically nonsense values when conducting a fit with
> > Paramfit? If you're seeing poor quality results, try fitting fewer
> > variables (for example, force constants only), adding more representative
> > or diverse input structures, or adding more dihedral terms. I usually fit
> > only force constants and set all phases to 0 or 180 to be consistent with
> > the rest of the forcefield.
> >
> > Sorry the code can be kind of difficult to use. I wrote it many years ago
> > and haven't had the time to make it more user-friendly. The usage
> tutorial
> > (
> > http://ambermd.org/tutorials/advanced/tutorial23/index.html) is probably
> > the best available reference for what the code can do.
> >
> > Hope this helps,
> > Robin
> >
> > On Wed, Nov 15, 2017 at 7:19 AM, viktor drobot <linux776.gmail.com>
> wrote:
> >
> > > I try to understand what energy paramfit returns. If I zeroed Kp for my
> > > term in frcmod, performed generation of rotational trajectory with this
> > > frcmod and then calculated energies with paramfit - will these energies
> > > contain all terms (including vdw and electrostatic) with the only
> > > exception? In other words, I want to obtain pure dihedral energy
> profile
> > > for my rotating group and apply FFT to it to extract significant
> dihedral
> > > terms and use them as initial assumptions in future paramfit work.
> > >
> > > 2017-11-15 15:14 GMT+03:00 viktor drobot <linux776.gmail.com>:
> > >
> > > > 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
> > > >> >
> > > >> > _______________________________________________
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> > > >> > AMBER.ambermd.org
> > > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > > >> >
> > > >> >
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> > > >>
> > > >
> > > >
> > > >
> > > > --
> > > > С уважением,
> > > > Дробот Виктор
> > > >
> > >
> > >
> > >
> > > --
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> > > Дробот Виктор
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Received on Fri Nov 17 2017 - 12:30:01 PST
