Ok I understand what is going on now -- thanks...
-
Jean-Paul Ebejer
Early Stage Researcher
On 16 January 2012 09:49, Greg Landrum <[email protected]> wrote:
> 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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