From: David L. <lon...@gm...> - 2011-12-19 19:54:46
|
On Mon, Dec 19, 2011 at 2:17 PM, Geoffrey Hutchison <ge...@ge...> wrote: >> Is there currently a GUI-based method to generate and view >> conformations of a molecule? Using the forcefield extension, I appear >> to be generating the conformers, but in View > Properties > Conformer >> Properties, only a single entry shows up. > > What conformer search are you using? The weighted search will just give you the lowest energy conformer, not generate new ones. Systematic searching should give you a set. Even with systematic and random search, I only get a single conformer in the properties dialog. Is this a bug or am I missing a step? (avogadro master and OB trunk) >> We would like to do this as part of a lab, so we need a GUI-based, >> student-friendly way to generate and compare conformations. Does >> anyone know if such a workflow is possible using existing tools? > > Without much coding, yes. Open Babel has a new (v2.3) conformer search framework, which should probably replace the weighted search and will generate multiple conformations. Better yet, you can either pick low-energy conformers, or a diverse set (i.e., maximizing RMSD differences). > > I just haven't had time to splice the new framework into the forcefield extension. I should be able to spend some time on this, since it will be related to my PI's lab course. I saw a GA search heuristic go into trunk, is this the one you mean? I can replace the current weighted search in the forcefield extension with that. Are the different fitness options already incorporated into OB, or can it take a user supplied fitness function callback? I can add some of these in if there's time. > I also have some ideas about manual dihedral scans, but that will need someone with more programming time. Check out the RotateSelection extension example (libavogadro/examples/thirdPartyExtensions/04-RotateSelection), I think it should be able to do dihedral scans without too much trouble, you might be able to modify that for a quick version. Dave |