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Hi, how to deal with a system containing metals？
And the protonation state of the atoms chelated with metals?
Also, how to relax water?
Thank you!
[7xrl](https://www.rcsb.org/structure/7xrl) a…
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Use `customElements.define` instead of `document.registerElement` see https://javascript.info/custom-elements
```
HTMLDocument.registerElement (file:///app/Pulsar/resources/app.asar/static/index.js:…
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## **Module/Workflow/Library affected**
openmm module
## **Expected behavior**
run openmm
## **Actual behavior**
[2024-11-13 08:33:27,417 libutil ERROR] No output models generated. Chec…
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We have discussed and agreed that `monitoring.yml` files should use the line
```
rss: ~
```
when no rss feed is available.
Some existing packages use an incorrect version of this:
``…
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When I run the run.sh in 3_train in example, there occurs the error below:
Traceback (most recent call last):
File "/public/home/yika/miniforge3/envs/deepH3/bin/deeph-train", line 8, in
sys.…
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`apm list --installed --bare > package-list.txt`
```
Sublime-Style-Column-Selection@1.7.2
atom-beautify@0.29.16
atom-easy-jsdoc@4.8.0
autoclose-html@0.23.0
autocomplete-modules@1.6.7
center-c…
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**Description**
I think I'm running into https://github.com/MobleyLab/chemper/issues/99 or a variant when I try to create the following:
```
from openff.bespokefit.schema.smirnoff import AngleS…
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The wiki says:
> Sella provides an interface that is compatible with the [ASE Optimizer class](https://wiki.fysik.dtu.dk/ase/ase/optimize.html) interface.
Trying to input `ase.filters.FrechetCel…
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### Thanks in advance for your bug report!
- [X] Have you reproduced issue in [safe mode](https://pulsar-edit.dev/docs/atom-archive/faq/sections/what-does-safe-mode-do.html)?
- [X] Have you used the …
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After pdb4amber, I can only get
HETATM 1 C ACE A 1 32.763 17.920 10.953 1.00 0.00 C
HETATM 2 O ACE A 1 31.579 18.240 11.127 1.00 0.00 O
HETA…