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From: Ismail, Mohd F. <farid.ou.edu>

Date: Tue, 13 Mar 2012 22:08:48 +0000

Dr. Kirschner,

Can I ask how did you calculate the MM part?

*******************************

Mohd Farid Ismail

Graduate Student

Dept. of Chemistry/Biochemistry

University of Oklahoma

Norman 73019

________________________________________

From: Karl N. Kirschner [kkirsch.scai.fraunhofer.de]

Sent: Thursday, February 09, 2012 3:25 AM

To: AMBER Mailing List

Subject: Re: [AMBER] Force Field Parameterization -- Torsion Potentials

Hi Ryan,

In regards to the partial atomic charges. I would recommend reading the following paper and visiting the R.E.D. group's website (http://q4md-forcefieldtools.org/RED):

F.-Y. Dupradeau, A. Pigache, T. Zaffran, C. Savineau, R. Lelong, N. Grivel, D. Lelong, W. Rosanski & P. Cieplak, The R.E.D. tools: Advances in RESP and ESP charge derivation and force field library building, Phys. Chem. Chem. Phys. 2010, 12, 7821-7839

The conformation I used was the minima at 180 degrees for the ESP QM calculations. Three ESP QM calculations were done, each using a different molecular orientation in x,y,z coordinate space of the 180 degree conformation. This is need due to slight differences that arise when the ESP places a grid around the molecule. The use of three orientation help make the partial atomic charges reproducible.

Cheers,

Karl

----- Original Message -----

From: "Ryan Pavlovicz" <pavlovicz.7.osu.edu>

To: "AMBER Mailing List" ambermd.org>

Sent: Wednesday, February 8, 2012 6:14:45 PM

Subject: Re: [AMBER] Force Field Parameterization -- Torsion Potentials

Hi Karl,

Thanks a lot for your help!

Although the MM profile seems to be the smaller of my two problems, I have

played around with the partial atomic charges that you obtained from your

three-conformation fit, and have found that using the charges you derived

increases my relative MM maximum at 0 degrees by 0.5 kcal/mol. This

ultimately helps lower that RMSD from the QM profile as show figure I link

to below:

https://docs.google.com/open?id=0BwkQMO2EgiyoZmU2NzYyYjctMmIxNS00MzM3LWI2MDEtMGU2N2RiYjJiNGM1

I am wondering which three 2,3-butanedione conformations you used for your

charge calculations.

Also, I am now playing around with regenerating my QM profile, which seems

to be the most important in recreating the results shown in Figure 3 of

Wang et al. I'll get back to you with the results when the computations

have completed. Thanks again, Karl!

-ryan

On Wed, Feb 8, 2012 at 8:11 AM, Karl N. Kirschner <

kkirsch.scai.fraunhofer.de> wrote:

*> Hi Ryan,
*

*>
*

*> I can basically reproduce your MM results and the Wang et al QM results.
*

*> However, I took a slightly different approach for the quantum calculations
*

*> and the partial atomic charges. Note that due to symmetry, one only needs
*

*> to do a heavy atom rotation from 0-180 degrees (I also did this in 30
*

*> degree increments). I wasn't able to do the single-point calculation at the
*

*> MP4 level, instead I opted for a larger basis set at the MP2 level.
*

*>
*

*> For the QM constraint optimization about the C-C-C-C torsion angle I used
*

*> MP2//6-31++G(d,p). I performed single-point calculations on these
*

*> geometries at MP2/aug-cc-pVDZ (i.e. MP2/aug-cc-pVDZ//MP2//6-31++G(d,p)).
*

*> For partial atomic charges I used R.E.D., with HF/6-31G(d) electrostatic
*

*> potential using the Connolly surface algorithm, and a 2 stage RESP fit
*

*> using weighting factors qwt=.0005/.001. (3 molecular orientations were used
*

*> in the R.E.D. calculations.) All of this was done using GAMESS.
*

*>
*

*> My partial atomic charges are slightly different than yours, but
*

*> ultimately I don't think it matters too much for the internal heavy atom
*

*> rotation of this molecule. Regardless, here are the charges:
*

*>
*

*> 1 C1 -0.7300 0.2420 0.0000 c 1 MOL 0.5239
*

*> 2 C2 0.7300 -0.2420 0.0000 c 1 MOL 0.5239
*

*> 3 C3 1.7980 0.8190 0.0000 c3 1 MOL -0.2739
*

*> 4 H4 1.6930 1.4560 0.8710 hc 1 MOL 0.0861
*

*> 5 H5 1.6930 1.4560 -0.8710 hc 1 MOL 0.0861
*

*> 6 H6 2.7700 0.3460 0.0000 hc 1 MOL 0.0861
*

*> 7 C7 -1.7980 -0.8190 0.0000 c3 1 MOL -0.2739
*

*> 8 H8 -1.6930 -1.4560 0.8710 hc 1 MOL 0.0861
*

*> 9 H9 -1.6930 -1.4560 -0.8710 hc 1 MOL 0.0861
*

*> 10 H10 -2.7700 -0.3460 0.0000 hc 1 MOL 0.0861
*

*> 11 O11 -0.9520 1.4110 -0.0000 o 1 MOL -0.5082
*

*> 12 O12 0.9520 -1.4110 -0.0000 o 1 MOL -0.5082
*

*>
*

*> Attached you can see the resulting potential energy curves. I can
*

*> essentially reproduce the gaff curve and your curve. What I noticed is that
*

*> the resulting molecular mechanics curve is extremely sensitive to the V2
*

*> parameter! By changing the parameter from 1.2 to 2.2 the resulting curve at
*

*> 0 degrees goes from a transition state to a high energy minima.
*

*>
*

*> Concerning the QM calculations, both MP2 calcuations have no local minima
*

*> at 30 degrees, which align well with Wang et al MP4 curve. It is clear that
*

*> the shape of this potential is dependent upon the basis set, and most
*

*> likely the theory level too. I would double check your 30 degree
*

*> conformation (perhaps there is an issue with the improper torsion geometry
*

*> about the ketone functionality).
*

*>
*

*> Concerning the RMSD. I obtain a lower RMSD (averaged over all 7
*

*> conformations, not just the minima) for gaff than for your parameter, which
*

*> is opposite of what you find. For comparison to my MP2//6-31++G(d,p)
*

*> geometries, I obtain an RMSD value of 0.056 for gaff, and 0.058 when using
*

*> your V2.
*

*>
*

*> I don't think this answers your question(s) directly, but I hope that
*

*> helps some :) .
*

*>
*

*> Cheers,
*

*> Karl
*

*>
*

*> ----- Original Message -----
*

*> From: "Ryan Pavlovicz" <pavlovicz.7.osu.edu>
*

*> To: "AMBER Mailing List" ambermd.org>
*

*> Sent: Tuesday, February 7, 2012 4:40:05 PM
*

*> Subject: [AMBER] Force Field Parameterization -- Torsion Potentials
*

*>
*

*> I am trying to do some force field parameterization for a ligand similar to
*

*> how GAFF was developed. As a test, I decided to first attempt to recreate
*

*> Figure 3 in Junmei Wang's 2004 paper, "Development and Testing of a General
*

*> Amber Force Field." This figure shows how well the the proper torsional
*

*> parameters help the dihedral profile of 2,3-butanedione match that
*

*> determined at MP4/6-311G(d,p)//MP2/6-31G*. I first scanned the c-c-c-c
*

*> dihedral angle at 30 degree intervals from -180 to 180 with Gaussian03:
*

*>
*

*> # MP2/6-31G* Opt=ModRedundant
*

*>
*

*> dihedral scan of 2,3-butanedione
*

*>
*

*> 0 1
*

*> C 0.432 0.806 1.762
*

*> ...
*

*> H -2.858 0.571 -1.527
*

*>
*

*> 1 5 3 2 -180.0 S 12 30.0
*

*>
*

*> Then the energies of the optimized MP2 geometries were calculated at
*

*> MP4/6-311G(d,p):
*

*>
*

*> # MP4/6-311g(d,p) SP
*

*>
*

*> Also, the ESP derived charges for the molecule were determined at HF/6-31G*
*

*> as mentioned in Wang et al.:
*

*>
*

*> # HF/6-31G*//HF/6-31G* pop=mk scf=tight iop(6/33=2) iop(6/42=6) test
*

*>
*

*> and fit to the atomic centers with the two-stage fit automated by
*

*> 'antechamber'. The resulting charges are found in the following link to a
*

*> prepi file created for the small molecule:
*

*>
*

*> 0 0 2
*

*>
*

*> This is a remark line
*

*> molecule.res
*

*> BDE INT 0
*

*> CORRECT OMIT DU BEG
*

*> 0.0000
*

*> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
*

*> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
*

*> 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
*

*> 4 C1 c3 M 3 2 1 1.540 111.208 180.000 -0.43474
*

*> 5 H1 hc E 4 3 2 1.084 90.423 -53.479 0.12751
*

*> 6 H2 hc E 4 3 2 1.080 34.705 -180.000 0.12751
*

*> 7 H3 hc E 4 3 2 1.084 90.423 53.437 0.12751
*

*> 8 C4 c M 4 3 2 1.506 143.914 -180.000 0.56915
*

*> 9 O2 o E 8 4 3 1.190 124.063 0.000 -0.51693
*

*> 10 C3 c M 8 4 3 1.538 116.849 180.000 0.56915
*

*> 11 O1 o E 10 8 4 1.190 119.088 0.000 -0.51693
*

*> 12 C2 c3 M 10 8 4 1.506 116.849 -180.000 -0.43474
*

*> 13 H4 hc E 12 10 8 1.084 110.176 -58.835 0.12751
*

*> 14 H5 hc E 12 10 8 1.084 110.154 58.874 0.12751
*

*> 15 H6 hc E 12 10 8 1.080 109.209 180.000 0.12751
*

*>
*

*>
*

*> LOOP
*

*>
*

*> IMPROPER
*

*> C1 C3 C4 O2
*

*> C2 C4 C3 O1
*

*>
*

*> DONE
*

*> STOP
*

*>
*

*> Finally the dihedral profile of the 2,3-butanedione was created in Amber9
*

*> using GAFF and the above prepi file with nmropt=1 to control the dihedral
*

*> angle with strong harmonic restraints:
*

*>
*

*> Minimization of the entire molecular system
*

*> &cntrl
*

*> imin=1, ncyc=9, maxcyc=500000, drms=0.0001,
*

*> ntpr=1, ntb=0, igb=0, cut=12,
*

*> scnb = 2.0, scee = 1.2,
*

*> nmropt=1
*

*> /
*

*> &wt type='END'
*

*> /
*

*> LISTOUT=POUT
*

*> DISANG=RST
*

*>
*

*> The following link contains my results compared to Figure 3 in Wang et al.
*

*> In general, my dihedral profile produced in Amber with GAFF is fairly close
*

*> to that used in Wang et al., however my ab initio dihedral profile is quite
*

*> different. I calculated a profile that is much more flat in the range from
*

*> -60 to 60 and much more steep in the other regions.
*

*>
*

*>
*

*> https://docs.google.com/open?id=0BwkQMO2EgiyoZWY0MWRjYTEtNTFjMC00NjNlLTg0MTUtM2MxZTExNjc5ZTVh
*

*>
*

*> I scanned the PK values for the V2 potential and found that based on my
*

*> calculation methods, a PK value of 2.2 resulted in the lowest RMSD between
*

*> the Amber and Gaussian calculated dihedral profiles (13 points from -180 to
*

*> 180). With PK=2.2, my calculated RMSD was 0.432. At PK=1.2, where Wang et
*

*> al. report their lowest RMSD of 0.2394, i calculate a RMSD of 1.285. As
*

*> you'll notice in the figure, by optimizing the dihedral profile based on
*

*> RMSD with only a V2 potential, i obtain a decent RMSD; however, the profile
*

*> is poor, with a pronounced local minimum at 0 degrees instead of a maximum!
*

*> Can anyone help point out where i may be going wrong in my attempt to
*

*> reproduce this figure/methodology? Thanks in advance for our help!
*

*>
*

*> -ryan
*

*> _______________________________________________
*

*> 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
*

*>
*

*>
*

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Received on Tue Mar 13 2012 - 15:30:02 PDT

Date: Tue, 13 Mar 2012 22:08:48 +0000

Dr. Kirschner,

Can I ask how did you calculate the MM part?

*******************************

Mohd Farid Ismail

Graduate Student

Dept. of Chemistry/Biochemistry

University of Oklahoma

Norman 73019

________________________________________

From: Karl N. Kirschner [kkirsch.scai.fraunhofer.de]

Sent: Thursday, February 09, 2012 3:25 AM

To: AMBER Mailing List

Subject: Re: [AMBER] Force Field Parameterization -- Torsion Potentials

Hi Ryan,

In regards to the partial atomic charges. I would recommend reading the following paper and visiting the R.E.D. group's website (http://q4md-forcefieldtools.org/RED):

F.-Y. Dupradeau, A. Pigache, T. Zaffran, C. Savineau, R. Lelong, N. Grivel, D. Lelong, W. Rosanski & P. Cieplak, The R.E.D. tools: Advances in RESP and ESP charge derivation and force field library building, Phys. Chem. Chem. Phys. 2010, 12, 7821-7839

The conformation I used was the minima at 180 degrees for the ESP QM calculations. Three ESP QM calculations were done, each using a different molecular orientation in x,y,z coordinate space of the 180 degree conformation. This is need due to slight differences that arise when the ESP places a grid around the molecule. The use of three orientation help make the partial atomic charges reproducible.

Cheers,

Karl

----- Original Message -----

From: "Ryan Pavlovicz" <pavlovicz.7.osu.edu>

To: "AMBER Mailing List" ambermd.org>

Sent: Wednesday, February 8, 2012 6:14:45 PM

Subject: Re: [AMBER] Force Field Parameterization -- Torsion Potentials

Hi Karl,

Thanks a lot for your help!

Although the MM profile seems to be the smaller of my two problems, I have

played around with the partial atomic charges that you obtained from your

three-conformation fit, and have found that using the charges you derived

increases my relative MM maximum at 0 degrees by 0.5 kcal/mol. This

ultimately helps lower that RMSD from the QM profile as show figure I link

to below:

https://docs.google.com/open?id=0BwkQMO2EgiyoZmU2NzYyYjctMmIxNS00MzM3LWI2MDEtMGU2N2RiYjJiNGM1

I am wondering which three 2,3-butanedione conformations you used for your

charge calculations.

Also, I am now playing around with regenerating my QM profile, which seems

to be the most important in recreating the results shown in Figure 3 of

Wang et al. I'll get back to you with the results when the computations

have completed. Thanks again, Karl!

-ryan

On Wed, Feb 8, 2012 at 8:11 AM, Karl N. Kirschner <

kkirsch.scai.fraunhofer.de> wrote:

_______________________________________________

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Tue Mar 13 2012 - 15:30:02 PDT

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