Ben Harland wrote:
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?
You must take into account the LJ and Coulomb interactions as well. You
should subtract these from your QC potential before fitting the torsion
potentials. It may well be that the resultant potential is closer to 180
once other effects are taken out.
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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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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