Method MMFF94 is available for a newly opened file only if it was selected beforehand

General Discussion Support
1

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I believe this to be a bug with Avogadro:
(Please describe your bug or issue)

Environment Information

Avogadro version: Windows (x64) • 2.0.0 • 115.2 MB • 01/04/2026
Operating system and version:

Edition Windows 11 Pro
Version 25H2
Installed on ‎15/‎12/‎2025
OS build 26200.8117
Experience Windows Feature Experience Pack 1000.26100.297.0
Processor Intel(R) Core™ Ultra 9 275HX (2.70 GHz)
Installed RAM 32.0 GB (31.4 GB usable)
System type 64-bit operating system, x64-based processor

Expected Behavior

All the force fields should be available for optimization or dynamics

Actual Behavior

When launching Avogadro by double-click on a molecule file, MMFF94 is not available, but only LJ and UFF.

Also, by launching Avogadro and then opening a molecule file, MMFF94 is not available, but only LJ and UFF.

To have MMFF94 available, you need to start Avogadro, then choose MMFF94, then open a molecule file.

Steps to Reproduce

start Avogadro, then open a molecule file, then check the available force fields: MMFF94 is not on the list

2

Force fields will only be available for a molecule if supported. MMFF94 only supports a limited number of elements and does not support radicals, etc.

So it would help a lot to know what molecule you’re trying to use for MMFF94.

It might be that choosing MMFF94, then opening a molecule, it’s still available (because you selected it) but that doesn’t mean it’s going to work.

3

Dear Prof. Hutchison,

thank you very much for the quick reply. I attach the molecule in the file below.

It contains C, H, N, P, Cl-, Zn2+ which should all be parametrized in MMFF94
( MMFF94 Force Field (mmff94) — Open Babel openbabel-3-1-1 documentation )

If Avogadro is launched alone, then MMFF94 is selected in the Auto Optimize Tool, then the molecule is opened, it is possible to optimize it with MMFF94 and perform dynamics.

Instead, if Avogadro is launched by double-clicking on the molecule, MMFF94 does not appear among the available Methods in the Auto Optimize Tool.

Again, thank you very much for your kind attention.
I’ll be happy to provide any further detail

Best regards
Corrado

test_build_13Apr2026.cjson (3.6 KB)

4

I highly suspect you’re getting UFF there. I’d need to check the code carefully for this particular case, but the current Avogadro code won’t take Zn as an available element for Zn.

Right, because it won’t show force fields that lack parameters.

In my experience, for a molecule like that, I would not trust MMFF94 parameters. Given the current state, I’d suggest using the xtb plugin to optimize a complex like that. You’ll get a much more accurate geometry from GFN2 than you could get from MMFF94, because it has a more accurate electrostatic model, is an approximate quantum mechanical method and thus doesn’t rely on particular bonding parameters, etc.

This file, for example is optimized with GFN2:
test_build_13Apr2026.cjson (99.8 KB)

5

Dear Geoff, thanks for the information and the file.

If I remove Zn, then launch Avogadro by double-clicking on the molecule, MMFF94 does appear, so you are definitely right on that.

On the other hand, when MMFF94 is selected in the Auto Optimize Tool, then the molecule with Zn is opened, the optimization with MMFF94 is clearly different from that with UFF.

Unless, when you say “you’re getting UFF there“ you mean that UFF is used just for Zn (maybe not really possible to have mixed FF?)

Again, thanks for your time and the very useful suggestion! I will try it right now

Cheers

Corrado

1 Like
6

Thanks - I’ll take a look. In this case, it works for you, but for many cases that would be a bad bug (e.g., if you tried that with Co or Ru or something)

No, UFF doesn’t mix well with other force fields. There are some with “compatible” parameters (e.g., GAFF and Amber) but that’s not supported in Avogadro right now.