Dear JP,
On Mon, Jan 16, 2012 at 10:32 AM, JP <[email protected]> wrote:
> Thanks Geoff It does help -- to at least understand that there are
> differences (by design),,,
>
> Greg, that is very close to how I calculate the energy... for further
> elucidation I have attached an example file (of 10 structures) -
> 10_conformers.sdf
>
> mol_h = AllChem.AddHs(molecule)
> ff = AllChem.UFFGetMoleculeForceField(mol_h)
> energy_value = ff.CalcEnergy()
Um, I guess the problem is that you aren't minimizing after you add the Hs.
>
> I get e values of:
>
> 83800.469
> 44774.061
> 25415192.307
> 381275.571
> 18381035.425
> 12314524.431
> 90759062.247
> 84522343316.997
> 622873.226
> 4083891061152.739
Here's what I get for your structures:
In [9]: s = Chem.SDMolSupplier('10_conformers.sdf')
In [10]: for m in s:
ff = AllChem.UFFGetMoleculeForceField(m)
print ff.CalcEnergy()
....:
57.7250683303
54.6722170905
57.6934954798
57.0448953622
53.4835515317
55.1642278098
59.8378911632
59.5829136442
57.0808359111
58.0636389016
And if you want to use Hs:
In [8]: for m in s:
mh = Chem.AddHs(m,addCoords=True)
ff = AllChem.UFFGetMoleculeForceField(mh)
ff.Minimize()
print ff.CalcEnergy()
...:
59.8306432912
57.6755187943
60.6158620191
59.2768931145
56.6452102597
57.3258031622
62.8687616587
64.0563558398
59.5371738291
62.0704717638
Best,
-greg
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