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
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Received on Wed Jun 25 2008 - 06:07:37 PDT
