> > Just to note, comp chem does a local optimisation. To do a global > optimisation you need to do a conformer search and locally optimise > each. With OB, what you're actually comparing is the accuracy of > MMFF94 geometries and those from B3LYP. This is already well studied. > > Yes, I know that this is well studied, but I am aiming to see whether OpenBabel does as well as CDK relative to a "sort of true" structure taken from a reference database and reoptimized with DFT in gas phase (and consequently, whether I should prefer one to the other for a particular set of cases), not whether MMFF does a comparable job to DFT in geometry optimization. Obviously if one of the toolkits shows a result that is considerably different from the other, two things could be happening: A) there were bugs in implementing the 0D to 3D conversion or B) one toolkit has a slightly more accurate/exhaustive geometry optimization technique (very hard to imagine). If A is the case, I will see large individual errors in geometries, and if B is the case, I will observe a consistent small difference. My primary concern is case A - that is, whether the three-dimensional geometries are properly assigned, given handling chiral centers and various other points where 3D geometry generation can go wrong.
If you have seen a comparison between the two (or more) toolkits along these lines or any sort of benchmarking studies, I would be very grateful if you could point me to them. Of course, an easier thing to do here is to try the "broken telephone" test - that is, whether all the canonical SMILES I feed OpenBabel's 3D generator will be the same as those obtained after converting the generated 3D geometries back into canonical SMILES... Speaking of conformational searches, I had been under the impression that some sort of rudimentary conformational analysis, as has been implemented in obconformer, was already taking place when I called gen3D - but from what you have said I am guessing that this is not the case and I would have to hack something together to enable this. In any case, thank you very much for your helpful comments!
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