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T019: Fix "No template found for residue 444 (03P)" #308

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merged 8 commits into from
May 22, 2023
Merged

T019: Fix "No template found for residue 444 (03P)" #308

merged 8 commits into from
May 22, 2023

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dominiquesydow
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@dominiquesydow dominiquesydow commented Dec 28, 2022 •
edited by mbackenkoehler
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Description

Fix problem described in #307
Check: https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template

Todos

Notable points that this PR has either accomplished or will accomplish.

  • Fix template problem - how?
  • Remove simtk from docstrings
  • Revert back to CI that tests all notebooks (not only T019)

Status

  • Ready to go

@dominiquesydow dominiquesydow changed the title Create new branch! T019: Fix template found for residue 444 (03P) Dec 28, 2022
@dominiquesydow dominiquesydow self-assigned this Dec 28, 2022
@dominiquesydow dominiquesydow added the bug Something isn't working label Dec 28, 2022
@dominiquesydow dominiquesydow changed the title T019: Fix template found for residue 444 (03P) T019: Fix "No template found for residue 444 (03P)" Dec 29, 2022
@dominiquesydow dominiquesydow linked an issue Dec 29, 2022 that may be closed by this pull request
T019: ValueError: No template found for residue 444 (03P) #307
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@dominiquesydow dominiquesydow mentioned this pull request Dec 30, 2022
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@dominiquesydow
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Hi @schallerdavid, @Mika-Le, @AndreaVolkamer, do you have any ideas why openmm cannot find a template for the ligand 03P anymore? The prepared ligand still looks good to me --- what am I missing?

@dominiquesydow dominiquesydow mentioned this pull request Dec 31, 2022
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dominiquesydow added a commit that referenced this pull request Dec 31, 2022
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CI: Temporarily ignore T019 until fixed in #308
43db85f
Base automatically changed from base-ci-env-fix to master December 31, 2022 02:29
This was referenced May 16, 2023
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@AndreaVolkamer
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@schallerdavid any idea on how to fix the template issue?

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Hi everyone,

sorry for missing this for so long.

I added some comments via NBReview. Can you see those?

@AndreaVolkamer
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AndreaVolkamer commented May 22, 2023 •
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@schallerdavid thanks I found them here: https://app.reviewnb.com/volkamerlab/teachopencadd/blob/t019-fix-ligand-template/teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb/#comment-2845559d

@mbackenkoehler can you incorporate this please?

@AndreaVolkamer AndreaVolkamer mentioned this pull request May 22, 2023
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@mbackenkoehler mbackenkoehler changed the base branch from master to dev May 22, 2023 10:22
@mbackenkoehler mbackenkoehler merged commit b9ea2d9 into dev May 22, 2023
@dominiquesydow dominiquesydow deleted the t019-fix-ligand-template branch May 22, 2023 19:37
@mbackenkoehler mbackenkoehler mentioned this pull request May 24, 2023
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T019: ValueError: No template found for residue 444 (03P)
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