- 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 00:32:33 +0300

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!

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Nov 14 2017 - 14:00:04 PST

Date: Wed, 15 Nov 2017 00:32:33 +0300

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

(image/png attachment: ______________________.png)

(image/png attachment: 02-______________________.png)

(image/png attachment: __________________________2017-11-15_00-00-37.png)

Custom Search