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Package for relative binding free energy calculations. See:
TIES 20: Relative Binding Free Energy with a Flexible Superimposition Algorithm and Partial Ring Morphing Mateusz K. Bieniek, Agastya P. Bhati, Shunzhou Wan, and Peter V. Coveney Journal of Chemical Theory and Computation 2021 17 (2), 1250-1265 DOI: 10.1021/acs.jctc.0c01179
The easiest way to install TIES is with conda:
conda install ties
You can use your own charges with the .mol2 format:
ties -l l1.mol2 l2.mol2 l3.mol2 --ligand-net-charge -2
A PDB will automatically assume the need for BCC charges:
ties -l left_coor.pdb right_coor.pdb -p protein.pdb -nc 0
For help use ties -h
Clone the repository:
git clone https://github.com/UCL-CCS/TIES20.git
It is simplest to use the same conda environment where ambertools was installed. Once in the right environment, go to the cloned directory and type:
conda env create -f environment.yml
conda activate ties
pip install .
This should install the dependancies and make ties available in the environment.
Please see the examples directory and test cases for more.
Conda can be used to easily install ambertools:
conda install ambertools -c conda-forge
Note that sqm in ambertools might need libgfortran. This can be installed with apt-get install libgfortran3. However, the conda version conda install libgfortran -c conda-forge should also work.
This should set the variable AMBERHOME which will be picked up on the fly.
Copyright (c) 2025, UCL CCS
Project based on the Computational Molecular Science Python Cookiecutter version 1.10.