Hi all,
I’m writing a Python script to screen a bunch of molecules, and for part of
that I would like to read in and optimize a geometry using OpenBabel’s
ForceField methods subjected to a couple constraints. I would like to obtain
the resulting forces for each atom from the optimization to use as an initial
cut off. Avagadro will print out force arrows during an optimization and I see
in the API documentation that functions exist to obtain the forces, however, I
keep getting an error when I try to implement this. For reference, I am using
OpenBabel 2.4.1 installed through conda.
Using the openbabel module with
--
conv = openbabel.OBConversion()
conv.SetInAndOutFormats('xyz','xyz')
mol = openbabel.OBMol()
conv.ReadFile(mol,'my_molecule.xyz’)
constraints = openbabel.OBFFConstraints()
constraints.AddAtomConstraint(1)
constraints.AddAtomConstraint(2)
forcefield = openbabel.OBForceField.FindForceField("UFF")
forcefield.Setup(mol, constraints)
forcefield.SetConstraints(constraints)
forcefield.ConjugateGradients(500)
forcefield.GetCoordinates(mol)
data = openbabel.toConformerData(mol.GetData(1))
f = data.GetForces()
--
I get this error:
--
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted
--
Can anyone shed any light on this and possibly point me in the right direction?
Thanks for your time,
Stephen
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