# Alchemical softening of imatinib bound to Abl

This example uses fused alchemical softcore potentials implemented in the [`alchemy`](https://github.com/choderalab/alchemy) package to relax the geometry of imatinib in the binding site of Abl kinase.
The ligand is not fully alchemically annihilated---only partially, so as to allow sampling barriers to be easily overcome.

## Manifest

* `soften-ligand.py` - example driver script for alchemically softening the ligand
* `setup/` - these files were automatically generated by YANK; they contain Amber `prmtop/inpcrd` files for the solvated complex, used here

## Usage

Make sure you have the omnia channel and `dev` label added to your conda path:
```bash
# Add omnia channel for stable omnia packages
- conda config --add channels omnia
# Add omnia dev channels to pick up `openmm 7.1.0` pre-release
- conda config --add channels omnia/label/dev
```
Install SAMS:
```bash
conda install --yes sams
```
Run the example:
```bash
python soften-ligand.py
```
