BAT version 2.3

New features in the BAT.py 2.3 version:

• TI calculations with Gaussian Quadrature (TI-GQ) for OpenMM

• Automatic determination of TI-GQ lambdas and weights using only the number of points as as input

• Choice of multiple restrained protein backbone sections

• Output of total simulation time of each calculation

• Automatic adjustment of solvation buffers when using the solv_shell option

• Additional sample systems and input files

• Inclusion of a quick installation guide for all needed dependencies, with a simplified command-oriented tutorial

BAT version 2.2

New features in the BAT.py 2.2 version:

• Support for proteins with multiple chains

• Inclusion of cobinders such as ions

• Additional water models

• Use of the lovoalign protein alignment software, replacing MUSTANG

• Compatibility with AMBER22

BAT version 2.1

New features on BAT 2.1:

• Merged components for the restraints, allowing all the of them to be attached or released using a single set of windows.

• Choice of retaining the ligand protonation, if already starting from a protonated pdb file for the docked pose.

• Choice of defining the ligand net charge manually, to help with the generation of partial atomic charges using Antechamber.

• Optimized simulation times and number of windows in the tutorial files, greatly reducing the computational cost of the ABFE calculations.

• Support for the OpenMM 7 simulation engine.

• A few bug fixes.

BAT version 2.0

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New features on BAT 2.0:

- Relative restraints between the receptor and the ligand (figure below), without the need for three fixed dummy atoms.

- Center of mass restraints on the receptor, and the bulk ligand when the SDR method is applied, so their internal degrees of freedom are not affected.

- Only two stages, equilibrium and free energy simulations. The preparation stage is no longer required, since the APR method is not available in the 2.0 version.

- Possible choice between a fixed number of waters, or fixed solvation buffers in the three cartesian axes.

- Automatic determination of the number of ions based on the chosen salt concentration.

- Simpler procedure to add new receptors.

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BAT version 1.0

Uses absolute positional restraints for the protein and ligand, with three fixed dummy atoms. Performs calculations using the double decoupling (DD), simultaneous decoupling and recoupling (SDR) and attach-pull-release (APR) methods.