A small note - just to be clear - these 10 structure I have attached in the
file have already undergone energy minimization using UFF with RDKit.
-
Jean-Paul Ebejer
Early Stage Researcher
On 16 January 2012 09:32, 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()
>
> 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
>
> For reference, using obenergy -ff UFF 10_conformers.sdf | grep "TOTAL
> ENERGY"
>
> TOTAL ENERGY = 1581.35605 kJ/mol
> TOTAL ENERGY = 1538.05680 kJ/mol
> TOTAL ENERGY = 1520.81917 kJ/mol
> TOTAL ENERGY = 1555.40200 kJ/mol
> TOTAL ENERGY = 1451.25485 kJ/mol
> TOTAL ENERGY = 1539.99455 kJ/mol
> TOTAL ENERGY = 1538.71850 kJ/mol
> TOTAL ENERGY = 1574.03694 kJ/mol
> TOTAL ENERGY = 1536.37672 kJ/mol
> TOTAL ENERGY = 1584.96023 kJ/mol
>
> -
> Jean-Paul Ebejer
> Early Stage Researcher
>
>
> On 16 January 2012 04:33, Geoff Hutchison <[email protected]>wrote:
>
>> >> 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)
>>
>> There are a couple of intentional differences. At one point, I offered to
>> give Greg a patch, but admit that I never did.
>>
>> 1) The UFF paper offers a unique cosine-based angle term. This allows for
>> octahedral complexes, but has the unfortunate consequence of a minimum of
>> the potential energy at 0 and 360 degrees. I have found this really
>> unsatisfactory, and modified the angle terms to give maxima at 0 and 360 --
>> otherwise angle terms will frequently fall into each other. I'm not sure
>> how other packages solve this, but I would frequently find optimizations
>> failing.
>>
>> 2) The UFF paper has some typos -- many of these have been corrected by
>> Towhee:
>> http://towhee.sourceforge.net/forcefields/uff.html
>>
>> 3) In order to better handle strange coordination numbers, Open Babel has
>> an empirical correction for the coordination number (e.g., 5-coordinate
>> phosphorus, etc.)
>>
>> There are some other minor points, such that the UFF in Open Babel can be
>> useful for VSEPR demonstrations to students (e.g., empirical terms for
>> 5-coordinate and 7-coordinate species, etc.)
>>
>> Hope that helps,
>> -Geoff
>
>
>
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