[gmx-users] oplsaa dihedral with minimum at 222 degrees
David van der Spoel
spoel at xray.bmc.uu.se
Tue May 30 07:58:04 CEST 2006
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 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
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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