I am preparing a topology for an opls-aa ATP molecule. It seems to me that
one does not yet exist. I am having difficulties with the dihedral
parameters: the OPLS-AA force field uses a RB-type function with a minimum
at 180 degrees, but our QC data describes a function symmetric about 222
degrees. Is there a way to accomodate this offset? Are there other
examples of molecules with an equilibrium dihedral angle other than trans?
I have also tried to fit this potential to a number of gromos-type periodic
functions with no luck.
Thanks in advance,
Ben Harland
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