Towards AshGC, a graph neural network charge model for Open Force Field

Biomolecular force fields typically model electrostatic interactions with point partial charges assigned using expensive ab initio or semi-empirical approaches, which scale poorly to large molecules such as proteins. While protein force fields typically encode pre-computed charges for standard residues, this approach cannot account for non- standard components like covalently bound ligands or post-translational modifications and assigning charges to these systems remains a non-trivial task. Open Force Field has been developing a graph neural network-based method for efficient assignment of self- consistent charges to both small and large molecules for Open Force Field force fields. This charge model, called AshGC, has been fit to produce charges of semi-empirical quality at low cost. Here we describe the model, its architecture, featurization, training process, and release plan. AshGC is currently available as a release candidate under the name "openff-gnn-am1bcc-0.1.0-rc.3.pt" and can be used with Open Force Field infrastructure.

Institutions

Publication Details

Journal
Zenodo (CERN European Organization for Nuclear Research)
Published
2025-06-30
DOI
https://doi.org/10.5281/zenodo.15770227
Citations
1
Primary Topic
Coleoptera Taxonomy and Distribution
Type
article
Field-Weighted Citation Impact
3.03
Controls
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article

Towards AshGC, a graph neural network charge model for Open Force Field

1 citations
Zenodo (CERN European Organization for Nuclear Research)
Coleoptera Taxonomy and Distribution
3.03
article

Towards AshGC, a graph neural network charge model for Open Force Field

article en
1 citations

Abstract

Biomolecular force fields typically model electrostatic interactions with point partial charges assigned using expensive ab initio or semi-empirical approaches, which scale poorly to large molecules such as proteins. While protein force fields typically encode pre-computed charges for standard residues, this approach cannot account for non- standard components like covalently bound ligands or post-translational modifications and assigning charges to these systems remains a non-trivial task. Open Force Field has been developing a graph neural network-based method for efficient assignment of self- consistent charges to both small and large molecules for Open Force Field force fields. This charge model, called AshGC, has been fit to produce charges of semi-empirical quality at low cost. Here we describe the model, its architecture, featurization, training process, and release plan. AshGC is currently available as a release candidate under the name "openff-gnn-am1bcc-0.1.0-rc.3.pt" and can be used with Open Force Field infrastructure.

Zenodo (CERN European Organization for Nuclear Research)
Memorial Sloan Kettering Cancer Center (US), University of Colorado Boulder (US), University of California, Irvine (US), Open Geospatial Consortium (US), Scientific Consulting Group (US), Open Molecular Software Foundation, Newcastle University (GB)
Industry, innovation and infrastructure
Openalex Percentile: Top 7%
Coleoptera Taxonomy and Distribution
3.03
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Towards AshGC, a graph neural network charge model for Open Force Field · Zenodo (CERN European Organization for Nuclear Research) (2025) | TGRS Research Map | TGRS