Ahh, I apologize, that was too short a message. What I want to do is perform regular organic solvent simulation. Since some of the densities do not match, I want to compare the result of MP2 calculation to the GAFF-based calculation. I have perform the calculation for the geometry with GAMESS. However, how do I get the GAFF-based structure using Amber? Do I just perform the minimization of 1 molecule?
*******************************
Mohd Farid Ismail
Graduate Student
Dept. of Chemistry/Biochemistry
University of Oklahoma
Norman 73019
________________________________________
From: Ismail, Mohd F. [farid.ou.edu]
Sent: Tuesday, March 13, 2012 5:08 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Force Field Parameterization -- Torsion Potentials
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
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Received on Tue Mar 13 2012 - 15:30:03 PDT
