Hi,
the dihedral parameters are not the only term that is taken into account
for the total energy calculation. Indeed, the 1-4 terms are not zero for
such a system. The dihedral parameters are just a decomposition of the
remaining energy term once you have taken into account the coulomb and
the vdW interactions in your molecule.
If you want to check the energy barrier, you have to perform a
calculation with all the force-field terms (especially 1-4 ones in your
case).
Hope this helps.
Jerome
On Tue, 2008-06-24 at 10:43 +0800, Q733 wrote:
> Dear Amber users:
>
> I constructed a forcefield for an organic molecule containing 81 atoms
> using the Amber 2003 united atom forcefield, and checked the energy
> difference of X-C2-C2-X
> dihedral between 0 and 180 degree .
>
> There are totally 3 sets of dihedral parameters:
> X -C2-C2-X 1 1.60 0.0 -3. Yang et
> al, 2005
> X -C2-C2-X 1 0.60 180.0 -2. Yang et
> al, 2005
> X -C2-C2-X 1 1.00 180.0 1. Yang et
> al, 2005
>
> I added all of them according to the formula: Etors=(PK/IDIVF)*(1
> +cos(PN*phi-phase)) and calculated the dihedral energy at 0 degree and
> 180 degree, which is 3.2 and 2 KJ respectively. The difference is only
> 1.2 kcal/mol, while in Amber8 manual on page 257 it is mentioned that
> the general energy barrier of H3-CT-CT-H3 is about 3 kcal/mol, I can
> not understand why there is such a huge difference.
>
> I also calculated the energy difference of 2-methyl-petane with the
> dihedral of -C2-C2- at 0 degree and 180 degree using Gaussian03, and
> kept other parts of the molecule optimized and fixed, the result is
> about 14.76 kcal/mol, but the total energy difference of
> 2-methyl-pentane calculated using 0 step of energy minimization using
> amber is about 9.76 kcal/mol. The energy does not match well.
>
> Is there anything wrong with my understanding or calculation ?
>
> Thanks very much in advance.
>
> Shanshan Qin
>
>
--
Jerome Golebiowski, PhD
LCMBA, team Chemometrics and Molecular Modeling
University of Nice, parc Valrose
06108 Nice Cedex2 France
tel : +33 (0)4 92 07 61 03
http://www.unice.fr/lcmba
http://www.unice.fr/lcmba/golebiowski
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Received on Wed Jun 25 2008 - 06:07:40 PDT
