Thanks very much for your prompt assistance, Noel and Geoffrey! This has solved my problem.
Take care, Stephen ________________________________ From: Geoffrey Hutchison <[email protected]> Sent: Tuesday, February 4, 2020 12:55 PM To: Shiring, Stephen B <[email protected]> Cc: [email protected] <[email protected]> Subject: Re: [Open Babel] Python: Getting atomic forces after a FF optimization 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. You definitely want to use Open Babel 3.0, e.g. success = ff.Setup(mol.OBMol) if not success: ff = pybel._forcefields["uff"] success = ff.Setup(mol.OBMol) if not success: sys.exit("Cannot set up forcefield") ff.ConjugateGradients(100, 1.0e-3) ff.GetCoordinates(mol.OBMol) gradients = ff.GetGradientPtr() print(type(gradients)) for atom in mol.atoms: grad = ff.GetGradient(atom.OBAtom) print(grad.GetX(), grad.GetY(), grad.GetZ()) Hope that helps, -Geoff
_______________________________________________ OpenBabel-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
