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Update FAQ on biopolymer force field #494

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mattwthompson opened this issue Jul 24, 2024 · 1 comment
Open

Update FAQ on biopolymer force field #494

mattwthompson opened this issue Jul 24, 2024 · 1 comment

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@mattwthompson
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This seems (~4 years?) out of date

Do you have plans to broaden your effort to include protein and biopolymer force fields?

As mentioned above, we have successfully applied for federal funding to allow us to broaden the scope of the Initiative beyond the Consortium-funded focus on small molecules and cover complex biomolecular systems. We would like to partner with the biopolymer force field community to build a family of fully consistent general biopolymer and small molecule force fields, with the goal of fully consistent handling of biopolymers and small molecules, including natural (proteins, RNA, DNA) and unnatural (e.g. peptoids) biopolymers, as well as posttranslational modifications and nonnatural amino acids. Handling of unusual nonnatural amino acids or bases can be a major headache with current force fields, but our approach will allow a single simple force field to consistently treat biopolymers and small molecules. This expanded effort is not within the current scope of Consortium funding, and would benefit from bringing in partners with significant expertise in biopolymer force field development.

We aim for our effort to be synergistic with, not competitive with, existing force field efforts, and we are seeking advice from the experts in the field who are a part of our OpenFF Initiative Advisory Board and others. We are always excited to support other efforts to seek funding for exciting new force field science—see Requesting Letters of Collaboration below if you would like us to demonstrate our support in your application for funding.

https://openforcefield.org/community/faq/

@mattwthompson
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This section in the versioning explainer is also out of date (there is no amber14SB.offxml and likely never will be), pointing to https://github.com/openforcefield/openff-amber-ff-ports?tab=readme-ov-file#installation or the mirrored information in docs.openforcefield.org

Biomolecular force fields:
amber14sb will be ported to amber14SB.offxml. After the first refit, biomolecular force field parameters will become a part of openff-x.y.z with documentation describing the details.

https://openforcefield.org/force-fields/versioning/

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