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Add support for ff19SB force field#406

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lohedges merged 25 commits intodevelfrom
feature_ff19sb
Jun 30, 2025
Merged

Add support for ff19SB force field#406
lohedges merged 25 commits intodevelfrom
feature_ff19sb

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@lohedges lohedges commented Jun 20, 2025

This PR builds off the new Sire CMAP feature to add support for the ff19SB force field. I've added tests to make sure that it can be used to parameterise a protein and that the resulting molecule contains a cmap property.

Supersedes and closes #398.

  • I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [y]
  • I confirm that I have added a test for any new functionality in this pull request: [y]
  • I confirm that I have added documentation (e.g. a new tutorial page or detailed guide) for any new functionality in this pull request: [y]
  • I confirm that I have permission to release this code under the GPL3 license: [y]

@lohedges lohedges requested a review from mb2055 June 20, 2025 13:11
@lohedges lohedges added the enhancement New feature or request label Jun 20, 2025
@lohedges lohedges temporarily deployed to biosimspace-build June 20, 2025 13:11 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build June 20, 2025 13:11 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build June 20, 2025 13:11 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build June 20, 2025 13:11 — with GitHub Actions Inactive
@lohedges lohedges had a problem deploying to biosimspace-build June 20, 2025 13:11 — with GitHub Actions Failure
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While parameterisation works, we need to think about water models to support ff19SB, e.g. adding support for OPC. This will need updates to the gmx solvate wrapper, as well as additional reference topologies in Sire for interconversion between AMBER and GROMACS representations.

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I've now added support for the OPC water model, which requires the feature_ff19sb branch of Sire. I'll use this for some test simulations to make sure things are okay.

@lohedges lohedges temporarily deployed to biosimspace-build June 27, 2025 11:45 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build June 27, 2025 11:45 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build June 27, 2025 11:45 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build June 27, 2025 11:45 — with GitHub Actions Inactive
@lohedges lohedges had a problem deploying to biosimspace-build June 27, 2025 11:45 — with GitHub Actions Failure
@lohedges lohedges temporarily deployed to biosimspace-build June 30, 2025 14:47 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build June 30, 2025 14:47 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build June 30, 2025 14:47 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to biosimspace-build June 30, 2025 14:47 — with GitHub Actions Inactive
@lohedges lohedges had a problem deploying to biosimspace-build June 30, 2025 14:47 — with GitHub Actions Failure
@lohedges lohedges merged commit f9e890f into devel Jun 30, 2025
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@lohedges lohedges deleted the feature_ff19sb branch June 30, 2025 15:27
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