Dear JP, On Mon, Apr 4, 2011 at 5:28 PM, JP <[email protected]> wrote: > Hi there, > > I am doing a UFFOptimizeMolecule - to optimize a molecule - is it > possible to get the final energy value for this?
You need to work directly with the force field if you want the energy: >>> ff = AllChem.UFFGetMoleculeForceField(mol_h) >>> ff.Minimize() 0 #<- 0 means that the minimization converged >>> ff.CalcEnergy() 1.3281838347010912 >>> > Details: I have a list of 50 conformers and I would like to sample > the conformational space (I do not want to have lots of similar > conformers). > I though I could find the 50 energy values, cluster in say 6 groups > and sample from each (different) group. > > Do you see any problems with this approach ? Though conformations that have different energies will have different structures, it is certainly possible to have similar energies and different structures. A better way to do this would be to cluster the conformations based on their RMSD to each other and then take representatives. The RDKit has general-purpose code for picking representatives from a set, take a look at section 5.5 of the Getting Started in Python document. For this application you would need to provide a different distij() function (one that calls AllChem.GetBestRMS). A note: the distance-geometry based conformation generator that the RDKit uses has a tendency to produce pretty diverse conformations "out of the box". -greg ------------------------------------------------------------------------------ Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
