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From: Junmei Wang <junmwang.gmail.com>

Date: Tue, 24 Jun 2008 20:45:42 -0500

The following is the emails between Balazs Jojart, David Case and me. Maybe

you are interested in this topic.

Junmei

Hi Dave,

Now I understand why the two figures are so different: my one is total

energies and Balazs' is the total energy minus Ebond minus Eangle minus

Enonbonded. As a matter of fact, X-c-c-X has a V2 term in gaff, and this is

consistent to Balazs's figure, which has minimum at -180, 180 and 0.

The attached pdf files have rotation profiles for GAFF, QM (total energy),

MM2 and MMFF. They are all quite similar. GAFF has similar rotational

barrier to QM, while MM2 and MMFF have much big barriers. The discrepancy

between Balazs' QM profile to Figure 3 in the paper may be caused by (1)

ZPE, (2) different protocols in scanning calculations. I am not sure if

Gaussian 03 has improved 'scan' or not. In Gaussian 98, 'scan' first

optimizes the structure and does single point calculations for every

conformations. However, I don't think this is an ideal protocol to generate

rotational profile. For Figure 3, I performed 'popt' with the involved

torsional angle frozen.

Best

Junmei

Hi Balazs,

I am sorry for not replying your email earlier. I didn't re-run the QM

calculations to verify your QM data, I just perform torsional angle scanning

using MM2 and MMFF force fields. I got similar profiles as the one in Table

3 of GAFF paper. I will double check this issue when I upgrade gaff to gaff2

or uaff (universal amber force field). Thank you very much for your work on

gaff development.

Please find the attached pdf file for my rotational profile calculations.

Best

Junmei

----- Original Message ----

From: Balazs Jojart <jojartb.pharm.u-szeged.hu>

To: junmwang.yahoo.com

Sent: Thursday, June 5, 2008 5:42:02 AM

Subject: gaff parametrization

Dear dr. Wang,

I wroe a mail directly to dr. Case yesterday, and he suggested me to

forward my message to you, because you prepared the torsional parameters

for the general amber forcefield.

You can read the mail as follows, and I attached the files, as well.

Dear dr. Case,

I write you diretly because you are the coresponding author of the

article 'Development and Testing of a General Amber Force Field'.

I started 3 or 4 weeks ago to learn the development philosophy of the

amber forcefield, especially the torsional parameter fitting.

I thought, the the paper mentioned above, is a good starting point,

because it contains the torsional profile of acethyl-acetone

(ch3-co-co-ch3).

Unfortunatelly, I wasn't able to reproduce the data (figure 3.)

I performed the following protocol:

(1) the small molecule (MOL) was prepeared using gaussview

(2) optimization was performed at the MP2/6-31G* level, anf frequency

calculations were also conducted. I found only one imaginary freqency,

but rotating 3 degree of a methyl rotor solved the problem.

(3) relax scan was performed on MOL with the following keywords:

MP2/6-31G* Opt(Z-matrix,maxcycle=100) nosym, and for the appropriate

dihedral angle : D2 179.97084591 S 11 -30.0

(4) I prepared the input files form the gaussian log file using the

gaussview program.

(5) MP4 single point calculations were performed with the following

keywords: MP4/6-311G**.

(6) the UMP4(SDTQ) energies were collected from the single point

calculations. (you can find it in the attached excel (GAFF_xccx.xls)

file in column D3:D14, the values were converted to kcalmol-1 --> column

E3:E14).

(7) for the lowest energy conformer optimization at the HF/6-31G* and

MEP calculation were performed (you can find the prepared prepi file as

attachment (MOL.prepi)).

(8) molmech minimization using AMBER 9 (input file min1.in), and the

appropriate dihedral angle was restrained during the minimization with a

100 force constant (RST).

(9) the BOND, ANGLE, VDW, ELE, 1-4 VDW and 1-4 ELE were collected form

the log file file (G:N).

(10) in the Amber8 manual a read the following :'Before Fitting the

torsional parameters, we must generate the energy profile for the

molecular mechanical nonbonded potential as was done for the quantum

potential, subtract this curve from the quantum curve, and ?t the

torsional potential to the difference potential'

(11) I calculated the MP4-MM(bond,angle,ele,vdw,1-4)[D18:D29] and

MP4-MM(ele,vdw,1-4) [D34:D45].

(12) the obtained curves are completly different compared to Figure 3 in

the article.

My qustetion are:

Did I made any mistake during the calculation? I don't understand the

parameter development strategy in amber?

For the X-c-c-X torsional term th V2=1.2 kcal/mol, multiplicity=4, phase

angle=180. It is not clear for me how came these values from Figure 3.

'PHASE = 180 degrees if an energy minimum is at 0 degrees.' 8form amber8

manual. As we can see on Figure 3 there is a maximum at 0 degree. The V

paranmeter is not the one-half of the barrier? n=4, which means the

there is 4 minimums when during the rotation from 0 to 360 degree.(AR

LEach book).

Etors can be calculated with the following equation:

summaVn/2(1+cos(n×phi-phase)). Am i right? Consider only the first trhee

term:

V1/2(1+(cos(1×phi-phase))+V2/2(1-(cos(2×phi-phase))+V3/2(1+(cos(3×phi-phase))

(as I read the article of Jorgensen: Development and Testing of the OPLS

All-Atom Force Field ... (J. Am. Chem. Soc. 1996, 118, 11225-11236).

Then where can we set up the multiplicity parameter? The 'n' parameters

are not the same in the equation? Beacuese in the Gaff paper the 'n' is

described as the multiplicity, but in the Jorgensen paper n is equalt to

n in the Vn term.

Can you give me some notes where I made a mistake during the calculation

and the protocol?

Your help will be very appreciated!!!

Thank you for your help in advance!

Balazs Jojart Ph.D.

University Of Szeged

Department of Chemical Informatics

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Received on Wed Jun 25 2008 - 06:07:56 PDT

Date: Tue, 24 Jun 2008 20:45:42 -0500

The following is the emails between Balazs Jojart, David Case and me. Maybe

you are interested in this topic.

Junmei

Hi Dave,

Now I understand why the two figures are so different: my one is total

energies and Balazs' is the total energy minus Ebond minus Eangle minus

Enonbonded. As a matter of fact, X-c-c-X has a V2 term in gaff, and this is

consistent to Balazs's figure, which has minimum at -180, 180 and 0.

The attached pdf files have rotation profiles for GAFF, QM (total energy),

MM2 and MMFF. They are all quite similar. GAFF has similar rotational

barrier to QM, while MM2 and MMFF have much big barriers. The discrepancy

between Balazs' QM profile to Figure 3 in the paper may be caused by (1)

ZPE, (2) different protocols in scanning calculations. I am not sure if

Gaussian 03 has improved 'scan' or not. In Gaussian 98, 'scan' first

optimizes the structure and does single point calculations for every

conformations. However, I don't think this is an ideal protocol to generate

rotational profile. For Figure 3, I performed 'popt' with the involved

torsional angle frozen.

Best

Junmei

Hi Balazs,

I am sorry for not replying your email earlier. I didn't re-run the QM

calculations to verify your QM data, I just perform torsional angle scanning

using MM2 and MMFF force fields. I got similar profiles as the one in Table

3 of GAFF paper. I will double check this issue when I upgrade gaff to gaff2

or uaff (universal amber force field). Thank you very much for your work on

gaff development.

Please find the attached pdf file for my rotational profile calculations.

Best

Junmei

----- Original Message ----

From: Balazs Jojart <jojartb.pharm.u-szeged.hu>

To: junmwang.yahoo.com

Sent: Thursday, June 5, 2008 5:42:02 AM

Subject: gaff parametrization

Dear dr. Wang,

I wroe a mail directly to dr. Case yesterday, and he suggested me to

forward my message to you, because you prepared the torsional parameters

for the general amber forcefield.

You can read the mail as follows, and I attached the files, as well.

Dear dr. Case,

I write you diretly because you are the coresponding author of the

article 'Development and Testing of a General Amber Force Field'.

I started 3 or 4 weeks ago to learn the development philosophy of the

amber forcefield, especially the torsional parameter fitting.

I thought, the the paper mentioned above, is a good starting point,

because it contains the torsional profile of acethyl-acetone

(ch3-co-co-ch3).

Unfortunatelly, I wasn't able to reproduce the data (figure 3.)

I performed the following protocol:

(1) the small molecule (MOL) was prepeared using gaussview

(2) optimization was performed at the MP2/6-31G* level, anf frequency

calculations were also conducted. I found only one imaginary freqency,

but rotating 3 degree of a methyl rotor solved the problem.

(3) relax scan was performed on MOL with the following keywords:

MP2/6-31G* Opt(Z-matrix,maxcycle=100) nosym, and for the appropriate

dihedral angle : D2 179.97084591 S 11 -30.0

(4) I prepared the input files form the gaussian log file using the

gaussview program.

(5) MP4 single point calculations were performed with the following

keywords: MP4/6-311G**.

(6) the UMP4(SDTQ) energies were collected from the single point

calculations. (you can find it in the attached excel (GAFF_xccx.xls)

file in column D3:D14, the values were converted to kcalmol-1 --> column

E3:E14).

(7) for the lowest energy conformer optimization at the HF/6-31G* and

MEP calculation were performed (you can find the prepared prepi file as

attachment (MOL.prepi)).

(8) molmech minimization using AMBER 9 (input file min1.in), and the

appropriate dihedral angle was restrained during the minimization with a

100 force constant (RST).

(9) the BOND, ANGLE, VDW, ELE, 1-4 VDW and 1-4 ELE were collected form

the log file file (G:N).

(10) in the Amber8 manual a read the following :'Before Fitting the

torsional parameters, we must generate the energy profile for the

molecular mechanical nonbonded potential as was done for the quantum

potential, subtract this curve from the quantum curve, and ?t the

torsional potential to the difference potential'

(11) I calculated the MP4-MM(bond,angle,ele,vdw,1-4)[D18:D29] and

MP4-MM(ele,vdw,1-4) [D34:D45].

(12) the obtained curves are completly different compared to Figure 3 in

the article.

My qustetion are:

Did I made any mistake during the calculation? I don't understand the

parameter development strategy in amber?

For the X-c-c-X torsional term th V2=1.2 kcal/mol, multiplicity=4, phase

angle=180. It is not clear for me how came these values from Figure 3.

'PHASE = 180 degrees if an energy minimum is at 0 degrees.' 8form amber8

manual. As we can see on Figure 3 there is a maximum at 0 degree. The V

paranmeter is not the one-half of the barrier? n=4, which means the

there is 4 minimums when during the rotation from 0 to 360 degree.(AR

LEach book).

Etors can be calculated with the following equation:

summaVn/2(1+cos(n×phi-phase)). Am i right? Consider only the first trhee

term:

V1/2(1+(cos(1×phi-phase))+V2/2(1-(cos(2×phi-phase))+V3/2(1+(cos(3×phi-phase))

(as I read the article of Jorgensen: Development and Testing of the OPLS

All-Atom Force Field ... (J. Am. Chem. Soc. 1996, 118, 11225-11236).

Then where can we set up the multiplicity parameter? The 'n' parameters

are not the same in the equation? Beacuese in the Gaff paper the 'n' is

described as the multiplicity, but in the Jorgensen paper n is equalt to

n in the Vn term.

Can you give me some notes where I made a mistake during the calculation

and the protocol?

Your help will be very appreciated!!!

Thank you for your help in advance!

Balazs Jojart Ph.D.

University Of Szeged

Department of Chemical Informatics

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" (in the *body* of the email)

to majordomo.scripps.edu

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