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Cannot set up force fields upon save


I’m a student trying to create some models for a research project on neurotransmitters interacting with functionalised polymers. When I save my progress and load it up however, the force field optimization and auto optimization doesn’t work at all.

The software says it’ll revert back to UFF, and that’s all it does. It just keeps reverting back to UFF every time I press ctrl+alt+o without actually working.

If somebody could please help me out with this I’d highly appreciate it. I really need this software to work for a few papers I mean to publish.

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I don’t quite understand what you’re trying to do, or what molecule you’re trying to optimize.

If you have the optimization set to use MMFF94 and have elements in your molecular that are not in MMFF94, it will naturally revert to UFF, a universal force field. That has nothing to do with saving or anything else - it will happen based on your molecule and the force field chosen in the options.

Can you post the molecule file?

What’s happening is when I load up a model I have created and saved in .cml, I cannot apply any force field optimizations to it, be it MMF94 or UFF, whereas the model was optimized in MMF94 before saving.

Here are some of the files I’ve been working on:

I am a new user and I encountered the same problem.
I built a model and I successfully optimized the geometry the first time.
Then I copied and pasted the model in a new file and I modified it by adding a new element.
I tried to launch the optimization but it failed and the message “cannot set the force field” appeared.
Please could you tell me how can I fix this issue?

Thanking you in advance.

It would help to know what the new element is, or have a link to the file. For example, the MMFF94 force field supports common organic elements, but not a very large subset (e.g., B or Se are not supported).

e.g., Why we can’t see 3-d structures of certain compounds on PubChem?

The element is sodium. First I optimized the EDTA geometry then I replaced one proton by a sodium and launched the UFF optimization but it did not work. What is the trick?

Can you upload the file?

Of course.
Here it is : https://mycore.core-cloud.net/index.php/s/zex9QdgUcXqsDhX

UFF optimization works just fine for me after replacing H atoms with Na.

Can you be a bit more specific about what you’re doing and what “it did not work” means (e.g., with a screenshot or something).

To be more specific, when I import or build a model, the optimization seems to work only once. When I closed the file and I reopen it, it become impossible to launch a further optimization.
I took a screen shot that you will find at: https://mycore.core-cloud.net/index.php/s/JGvZhIn8jYbdXMR

Thanks for giving your time.