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

From: Lorenzo Gontrani <l.gontrani.caspur.it>
Date: Thu, 9 Feb 2012 09:47:43 +0100

Dear Ryan, I have a question for you. As far as I know (look at some
literature by Jorgensen and A. Padua, for instance), the torsional
profile should be fit to the difference between ab initio profile and
MM profile (both with the torsion under study frozen), to subtract the
1,4 terms of the force field. I suppose that this is done implicitly
in GAFF parametrization, by using Wang's code PARMSCAN. But maybe I am
wrong.

Best regards

Lorenzo

2012/2/7 Ryan Pavlovicz <pavlovicz.7.osu.edu>:
> 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



-- 
=======================================
 Lorenzo Gontrani
 Research associate of EDXD group
 University of Rome "La Sapienza"
 GSM +39 338 7615798
 Email l DOT gontrani AT caspur DOT it
 Webpage: http://webcaminiti/gontrani.html
 =======================================
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 09 2012 - 01:00:03 PST
Custom Search