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.
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:
pip install .
This should install the dependancies and make ties available in the environment. For help use:
ties -h
I recommend renaming the molecules first manually:
ties rename -l left_coor.pdb right_coor.pdb
Then in the simplest case use the BCC charges. In the following example the net charge is set to -2:
ties create -l left_coor.pdb right_coor.pdb -p protein.pdb -nc -2
The protein is not necessary:
ties create -l left_coor.pdb right_coor.pdb -nc -2
You can use your own charges with the .mol2 format:
ties create -l l1.mol2 l2.mol2 l3.mol2 -nc -2
Please see the examples folder with more cases.