# How long it takes for conformer search? **URL:** \ **Category:** Support\ **Created:** [October 8, 2026, 8:03pm UTC](https://discuss.avogadro.cc/t/how-long-it-takes-for-conformer-search/7545 "2026-10-08T20:03:57Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![ywoldman](https://discuss.avogadro.cc/letter_avatar_proxy/v4/letter/y/9de053/32.png) [@ywoldman](https://discuss.avogadro.cc/u/ywoldman)\ **Post date:** [October 8, 2026, 8:03pm UTC](https://discuss.avogadro.cc/t/how-long-it-takes-for-conformer-search/7545/1 "2026-10-08T20:03:58Z")
(Please describe your bug or issue) ## Environment Information Avogadro version: 2 Operating system and version: Windows 11 I am new to Avogadro (just started it today), so, sorry, if the question sounds silly: about how long the conformer search should run? Just ballpark: hours, days? And how do I know it is really running and not stuck somewhere? Molecule: C22H26BF2N8O14P3S, on laptop Intel i7, 1.7 GHz. Search parameters: MMFF94, convergence 10^-6u, steps limit 2500, 100 conformers, 25 steps per conformer, weighted rotor search. Thank you! ## Expected Behavior ## Actual Behavior ## Steps to Reproduce Please upload files if appropriate here (or via file-sharing service like Dropbox or Pastebin) ---
**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\ **Post date:** [October 8, 2026, 10:29pm UTC](https://discuss.avogadro.cc/t/how-long-it-takes-for-conformer-search/7545/2 "2026-10-08T22:29:35Z")
That’s a fairly large molecule. Typically I monitor conformer search based on the number of rotatable bonds. But the question is **what kind of search did you start**? Open Babel (through Avogadro) supports several different options, including systematic search, which would be pretty exhaustive. ---
**Author:** ![Thomas](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/thomas/32/3403_2.png) [@Thomas](https://discuss.avogadro.cc/u/Thomas)\ **Post date:** [October 12, 2026, 9:13pm UTC](https://discuss.avogadro.cc/t/how-long-it-takes-for-conformer-search/7545/3 "2026-10-12T21:13:30Z")
[Pubchem](https://pubchem.ncbi.nlm.nih.gov/) is one large public database, if you know an identifier like the chemical (English) name, CAS registry number; InChI or SMILES string you can look up records. If small enough, and “organic enough” (i.e., salts like phosphates do not count), chances are that there already is _a_ conformer to start with as 3D conformer. See for instance [glucose](https://pubchem.ncbi.nlm.nih.gov/compound/79025#section=3D-Conformer&fullscreen=true) with such data, and [mycolactone](https://pubchem.ncbi.nlm.nih.gov/compound/5282079) with an explicit `Conformer generation is disallowed since too many atoms, too flexible`. It needn’t be the conformer of lowest energy, and the conformer is the result of an affordable level of computation (MMFF94s force field, for details in J Cheminform (doi: [10.1186/1758-2946-3-32](https://doi.org/10.1186/1758-2946-3-32), open access), but depending on what you want to do _good enough_ for a display on a poster, or serve as a _starting point_ for additional work. If you don’t want to save the .sdf generated by PubChem on the web site itself, Avogadro2 offers a _download by name_, too. If you need a batch of conformers about multiple molecules, a programmatic approach (for instance [pubchempy](https://github.com/mcs07/pubchempy) and [cirpy](https://github.com/mcs07/CIRpy)) may more suitable. The example of glucose is one of the rare instances where pubchem provides multiple conformers per record. ---
**Author:** ![ywoldman](https://discuss.avogadro.cc/letter_avatar_proxy/v4/letter/y/9de053/32.png) [@ywoldman](https://discuss.avogadro.cc/u/ywoldman)\ **Post date:** [October 13, 2026, 2:03am UTC](https://discuss.avogadro.cc/t/how-long-it-takes-for-conformer-search/7545/4 "2026-10-13T02:03:51Z")
Thank you! As far as I understood, it is Monte-Carlo search (weighted rotor). Looking at the thread from July on the same topic, I suspect the search simply does not work, because nothing happens, and conformer analysis stays dim. The molecule is fluorescently labeled GTP. The thing I am trying to figure out if there is any chance for stacking BODIPY and guanine and if it gives any sizeable dip in energy ---
**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\ **Post date:** [October 13, 2026, 12:17pm UTC](https://discuss.avogadro.cc/t/how-long-it-takes-for-conformer-search/7545/5 "2026-10-13T12:17:38Z")
> [@ywoldman](#): > > I suspect the search simply does not work Please try a [nightly build](https://avogadro.cc/install/) - there are continuous bug fixes, including in the conformer search. The current builds are essentially pre-releases of v2.1 which will be released on 23 October. > [@ywoldman](#): > > The thing I am trying to figure out if there is any chance for stacking BODIPY and guanine and if it gives any sizeable dip in energy That’s going to be a tricky calculation. I would suggest at the least using the `xtb` program (or plugin). Standard force fields do not give accurate \pi-\pi stacking energetics. Personally, I’d rather approximate the potential BODIPY - guanine complex and then hand it off to `xtb` and then a DFT program like ORCA to optimize the geometry before determining energetics, e.g., [2.11. Counterpoise Corrections — ORCA 6.1.1 Manual](https://orca-manual.mpi-muelheim.mpg.de/contents/essentialelements/counterpoise.html) ---
**Author:** ![Thomas](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/thomas/32/3403_2.png) [@Thomas](https://discuss.avogadro.cc/u/Thomas)\ **Post date:** [October 13, 2026, 9:39pm UTC](https://discuss.avogadro.cc/t/how-long-it-takes-for-conformer-search/7545/6 "2026-10-13T21:39:38Z")
@ywoldman Some of force field methods are not prepared (parametrized) for boron (BODIPY) at all. The somewhat «salty / partially ionic character» of a charged BODIPY (after the treatment with \ce{BF3 \times Et2O}) could be an additional reason a force field based conformer search will not work. For pubchem – just checked again – both criterion 3 and 4 would be in opposition to run an optimization with their MMFF94s if boron is in place. I don’t know if substitution of the \ce{BF^-2} moiety by a methylene bridge _as temporary placeholder_ during an exhaustive conformer search on side chains were permissible. ---
**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\ **Post date:** [October 13, 2026, 11:33pm UTC](https://discuss.avogadro.cc/t/how-long-it-takes-for-conformer-search/7545/7 "2026-10-13T23:33:44Z")
Open Babel will switch to UFF for conformer searches because of the boron. And it’ll be okay, but if you’re looking to understand pi-pi stacking, it’s good to at least use something like `xtb-GFN2` ---
**Author:** ![ywoldman](https://discuss.avogadro.cc/letter_avatar_proxy/v4/letter/y/9de053/32.png) [@ywoldman](https://discuss.avogadro.cc/u/ywoldman)\ **Post date:** [October 15, 2026, 4:27pm UTC](https://discuss.avogadro.cc/t/how-long-it-takes-for-conformer-search/7545/8 "2026-10-15T16:27:24Z")
Thank you! I will do that. ---
**Author:** ![Thomas](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/thomas/32/3403_2.png) [@Thomas](https://discuss.avogadro.cc/u/Thomas)\ **Post date:** [October 15, 2026, 7:53pm UTC](https://discuss.avogadro.cc/t/how-long-it-takes-for-conformer-search/7545/9 "2026-10-15T19:53:04Z")
> [@ghutchis](#): > > Open Babel will switch to UFF for conformer searches because of the boron. Either I wasn’t aware of, or (more probable) I forgot the implemented logic of “openbabel’s fallback is UFF, and if necessary (e.g., for lack of parametrization) force field X is replaced by UFF”. With the archetypical [BODIPY](https://en.wikipedia.org/wiki/BODIPY), I run ```bash $ obabel -:'[B-]1(N2C=CC=C2C=C3[N+]1=CC=C3)(F)F' -h --gen3d -osdf ``` without an issue – which supports one part of your statement. I then run ```bash obabel -:'[B-]1(N2C=CC=C2C=C3[N+]1=CC=C3)(F)F' -h --gen3d --ff MMFF94 -osdf ``` which by [MMFF94 Force Field (mmff94) — Open Babel openbabel-3-2-0 documentation](https://openbabel.org/docs/Forcefields/mmff94.html) should preferentially issue a note, because boron is not one of the explicitly mentioned atoms. However, obabel (version 3.2.0 in Linux Debian) smoothly generates a .sdf, without any issue report to the CLI, nor non-blocking warning (like “kekulization failed”). If this were an example “implicitly, openbabel replaces the force field by UFF”, I would welcome - a reminder “actually, UFF serves as fallback automatically activated by the program” (wording here only is a doodle) in openbabel’s [Universal Force Field (uff) — Open Babel openbabel-3-2-0 documentation](https://openbabel.org/docs/Forcefields/uff.html). - a note like “instead of selected MMFF94, the optimization used UFF” to `stderr` / `2>` if obabel is run on the CLI - if an optimization in Avogadro2 relies on openbabel’s logic .and. openbabel identifies the need to favor UFF over user selected MMFF94, a little note in Avogadro2 equally were welcome as feedback to the user.