Ok problems solved from last post, I was missing the OBBuilder part (see
below for ethane from smiles). I think this should now be the same as what
gen3d does but with the python openbabel commands.
import openbabel
mol = openbabel.OBMol()
cv = openbabel.OBConversion()
cv.SetInAndOutFormats('smi', 'mol2')
cv.ReadString(mol, 'cc')
bd = openbabel.OBBuilder()
bd.Build(mol)
mol.SetDimension(3)
mol.AddHydrogens()
ff = openbabel.OBForceField.FindForceField("MMFF94")
ff.Setup(mol)
ff.SteepestDescent(250, 1.0e-4)
ff.WeightedRotorSearch(200, 25)
ff.ConjugateGradients(250, 1.0e-6)
ff.UpdateCoordinates(mol)
I ran two variations of the above (changing the opt criteria and number of
steps etc) and then used the coordinates to do gaussian optimization runs
(b3lyp/6-311G(d)). For one molecule I got quite different values because it
had gone into a more contorted shape.
- If time is not an issue, any suggestions on an optimal routine for the
above code?
- Would a systematic rotor search be more reliable (SystematicRotorSearch)?
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