Saving Conformer in PDB format

Dear all,

I am naive to Avogadro and looking for a help in saving pdb files of the conformations generated during the Conformer search. I am loading a PDB file and then setting up conformer search (Extensions -> Molecular Mechanics --> Conformer Search). How can I save all those conformers my PDB/Mol2 file which are shown on the viewer during the search.

Sorry for asking such a basic question.


At the moment, it’s not possible to save all conformers to one file. You can go through the conformers one at a time and save them to separate files.

If this is something you’re doing repeatedly, I’d suggest using Open Babel directly (which is what Avogadro uses for the conformer search):