OpenFF 2.2.1 Relative Binding Free Energy Benchmarks

OpenFF 2.2.1 Relative Binding Free Energy Benchmarks Overview Relative binding free energy benchmarks of the openff-2.2.1 release using the JACS set from (https://github.com/OpenFreeEnergy/IndustryBenchmarks2024). Contents Benchmark variants The following benchmark variants were run: * `openff-2.2.1_elf10`: simulations using OpenFF 2.2.1 and AM1BCCELF10 charges using the OpenEye Toolkit. * `openff-2.2.1_nagl`: simulations using OpenFF 2.2.1 and AshGC v0.1rc3 charges * `openff-2.2.1_am1bcc`: simulations using OpenFF 2.2.1 and AM1BCC charges calculated using ambertools. Please note that these charges were not assigned to the input conformer, but rather a conformer that was generated at charge assignment time via RDKit through the OpenFF toolkit. RBFE data The `data` folder contains all the ddG data for each transformation in each set. These are stored as TSV files within subdirectories for each system in the JACS set. Per system data files These are stored as TSV files within subdirectories for each system in the JACS set.Reference CSV data (labelled as `{system}_ref.csv`), taken from the Ross et al. 2023 dataset (https://github.com/schrodinger/public_binding_free_energy_benchmark)can alsos be found. Aggregate dG and ddG files CSV files with all the dG and ddG values for all datasets can be found in `data`. Simulation details * All simulations were carried out using the RelativeHybridTopology protocol in OpenFE v1.4.* Mappings were created using Kartograf, these are the same as those used in the OpenFE industry benchmarks.* Transformation edges were created using Lomap, these are the same as those used in the OpenFE industry benchmarks.* Simulations used openfe default settings, except the following: * Dodecahedron solvent box with 1 nm padding in complex and 1.5 nm padding in solvent * 2.5 ps HREX exchange rate * 0.9 nm short range interaction cutoffOpenFF 2.2.1 相对结合自由能基准测试集 概述 本基准测试集基于OpenFF 2.2.1版本构建，采用来自https://github.com/OpenFreeEnergy/IndustryBenchmarks2024的JACS数据集开展相对结合自由能计算。 内容 基准测试变体 本次测试包含以下三类基准变体： * `openff-2.2.1_elf10`：采用OpenFF 2.2.1力场与经OpenEye Toolkit计算的AM1BCCELF10电荷完成模拟。 * `openff-2.2.1_nagl`：采用OpenFF 2.2.1力场与AshGC v0.1rc3电荷完成模拟。 * `openff-2.2.1_am1bcc`：采用OpenFF 2.2.1力场与经AmberTools计算的AM1BCC电荷完成模拟。请注意，此类电荷并未直接赋予输入构象，而是通过RDKit结合OpenFF工具包在电荷分配阶段生成的构象上完成分配。 RBFE数据 `data`文件夹包含所有数据集下各转化过程的全部ddG（结合自由能差）数据，这些数据以TSV格式存储于JACS数据集每个体系对应的子目录中。 单体系数据文件 此类数据同样以TSV格式存储于JACS数据集各体系的子目录中。此外还可获取取自Ross等人2023年数据集（https://github.com/schrodinger/public_binding_free_energy_benchmark）的参考CSV数据，命名格式为`{system}_ref.csv`。 聚合dG与ddG文件 包含所有数据集全部dG（结合自由能）与ddG数值的CSV文件可在`data`文件夹中获取。 模拟细节 * 所有模拟均采用OpenFE v1.4中的RelativeHybridTopology（相对混合拓扑）协议完成。 * 配体映射通过Kartograf工具生成，与OpenFE行业基准测试中使用的映射完全一致。 * 转化边（Transformation edges）通过Lomap工具生成，与OpenFE行业基准测试中使用的转化边完全一致。 * 模拟采用OpenFE默认设置，仅对以下参数进行了调整： - 采用十二面体溶剂盒：复合物体系溶剂填充间距为1 nm，纯溶剂体系为1.5 nm。 - HREX（副本交换）交换速率为2.5 ps。 - 短程相互作用截断半径为0.9 nm。