Dear JP,
On Fri, Jan 13, 2012 at 2:52 PM, JP <[email protected]> wrote:
>
> any comments about the second part of my query?
>
> "Also, any ideas what the energy units returned from ff.CalcEnergy() are?"
Should be kcal/mol; that's what the parameters from the UFF papers are
expressed in.
> The UFF values vary wildly from the ones offered by obenergy using UFF
> forcefield (this doesn't mean they are wrong of course, just want to
> understand why)
>
> OBenergy UFF (kJ/mol)
> TOTAL ENERGY = 603.32957 kJ/mol
> TOTAL ENERGY = 582.35037 kJ/mol
> TOTAL ENERGY = 483.29385 kJ/mol
> TOTAL ENERGY = 504.88763 kJ/mol
> TOTAL ENERGY = 555.16601 kJ/mol
> TOTAL ENERGY = 579.55593 kJ/mol
> TOTAL ENERGY = 581.58096 kJ/mol
> TOTAL ENERGY = 557.90448 kJ/mol
> TOTAL ENERGY = 532.21012 kJ/mol
> TOTAL ENERGY = 503.59585 kJ/mol
>
> RDKit Calc Energy (UFF) for exactly the same molecules...
> 16700300.472
> 154163.203
> 132597.990
> 124078.437
> 140688.066
> 4863030.479
> 20278658.428
> 3690505.452
> 145837.684
> 150862.539
>
> Some of the values I see for other molecules are huge - 4083891061152.739
> (but this is not the case when I use obenergy to calculate the energy
> values)
Those numbers all look much, much too big to me. How did you calculate them?
Here's a quick demo showing that the numbers aren't always huge:
In [18]: m = Chem.MolFromSmiles('CC1CCC1')
In [19]: mh = Chem.AddHs(m)
In [20]: AllChem.EmbedMolecule(mh)
Out[20]: 0
In [21]: ff =AllChem.UFFGetMoleculeForceField(mh)
In [22]: ff.CalcEnergy()
Out[22]: 30.062114232394034
In [23]: ff.Minimize()
Out[23]: 0
In [24]: ff.CalcEnergy()
Out[24]: 25.309049342130905
Best,
-greg
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