Dear All,
Recently I have been assessing some ligand conformations from crystal
structures to identify any non-ideal bond lengths, angles, torsions, or
non-bonded contacts.
What I am doing at the moment is adding some positional constraints to the
crystallographic heavy atom positions, and calculating the energy before and
after minimisation:
>>> m = Chem.MolFromMolFile('input.mol')
>>> mh = AllChem.AddHs(m, addCoords=True)
>>> mp = AllChem.MMFFGetMoleculeProperties(mh, mmffVariant='MMFF94s')
>>> ff = AllChem.MMFFGetMoleculeForceField(mh, mp)
>>> ff.CalcEnergy()
This gives the 'raw' energy.
>>> for atom in mh.GetAtoms():
>>> if not atom.GetAtomicNum() == 1:
>>> idx = atom.GetIdx()
>>> ff.MMFFAddPositionConstraint(idx, maxDispl=0.5, forceConstant=100)
>>> ff.Minimize(maxIts=10000)
>>> ff.CalcEnergy()
And this gives the energy after applying a moderate restraint (100 kcal/mol,
with a maximum displacement of 0.5 A).
So I think this is ok(?), and I can compare the two energies and inspect the
conformations visually.
What I was wondering was whether there is a way of obtaining the individual
energy terms (ie each bonded and non-bonded term, angle, and torsion)?
Because what I'd really like to do is identify the areas of the molecule that
contribute the most to the pre- and post- minimisation energy difference.
Any suggestions would be greatly appreciated!
Kind regards
James
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