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
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> 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
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Received on Thu Feb 09 2012 - 01:00:03 PST
