Thanks very much for your prompt assistance, Noel and Geoffrey!
This has solved my problem.
Take care,
Stephen
________________________________
From: Geoffrey Hutchison <geoff.hutchi...@gmail.com>
Sent: Tuesday, February 4, 2020 12:55 PM
To: Shiring, Stephen B <sshir...@purdue.edu>
Cc: openbabel-disc...@lists.sf.net <openbabel-disc...@lists.sf.net>
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
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