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
10_conformers.sdf
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