Dear Marshall, On Wed, Mar 4, 2009 at 8:34 AM, Marshall Levesque <[email protected]> wrote: > Does the number "1" after I try to optimize the molecule mean that there was > an error? > ####### >>>> m = >>>> Chem.MolFromSmiles('Clc1ccc(C=CC(=O)OC(P(=O)(OC2CC(CCC2C)C(C)C)OC2CC(CCC2C)C(C)C)c2cccnc2)c(Cl)c1') >>>> AllChem.EmbedMolecule(m) > 0 >>>> AllChem.UFFOptimizeMolecule(m) > 1 > #######
Nope, it just means that the optimization didn't converge. Try calling UFFOptimizeMolecule again or calling it with a higher value for maxIters. I will update the docs to include this information -greg
