I've successfully used the UFF force field to minimize an OBMol. I'm
now trying to use the Gaff, Ghemical and MMFF94 force fields, but none
will work.
...
I have read a SMILES in and (unlike earlier) am beginning with zero
positions for all atoms.
Well, you haven't said what type of molecule
Hi all,
I'm having issues with OBForceField.
I perform a crude layout of a SMILES string using a simulated
annealing method. I then pass the resulting structure to an
OBForceField instance to generate more accurate geometry. However, the
coordinates in the OBMol operated on remain the same after
..whoops, that's FOR_ATOMS_OF_MOL of course, just a typo (!).
On 31 July 2010 23:43, N David Brown hubd...@googlemail.com wrote:
Hi all,
I'm having issues with OBForceField.
I perform a crude layout of a SMILES string using a simulated
annealing method. I then pass the resulting structure
Did you call OBForceField::GetCoordinates after minimizing? The
forcefield works on a copy of the molecule so you have to get the
updated coordinates explicitly.
On Sun, Aug 1, 2010 at 12:44 AM, N David Brown hubd...@googlemail.com wrote:
..whoops, that's FOR_ATOMS_OF_MOL of course, just a typo
I didn't call that function, no. Many thanks, Tim.
It might be worth exemplifying this in at least one of the examples in
the API documentation to save others the same confusion (or maybe it's
just me!).
David
On 1 August 2010 00:02, Tim Vandermeersch tim.vandermeer...@gmail.com wrote:
Did
