This collection of python command line functions is designed with the aim to facilitate a robust and fast setup of FEP calculations for the software package Q. These modules use python 3, python 2 is no longer supported, and an old version of the code using python 2 is now only available in the python2 branch.
This package includes at the moment two main modules:
-
QligFEP.py: module to generate ligand FEP calculations using a dual topology approach, see Jespers et al. (https://doi.org/10.1186/s13321-019-0348-5).
-
QresFEP.py: module to generate protein FEP calculations using a single topology approach, see Jespers et al. (https://doi.org/10.1021/acs.jctc.9b00538).
Future versions will include QLIE, dual topology QresFEP and several translation tools for new forcefields (at the moment we support opls, charmm,amber and openFF).
A few toplevel scripts are included in the scripts folder to facilitate high throughput setup. Additionally, a tutorials folder is included with a detailed description of the setup procedure as published in Jespers et al. (QresFEP/QligFEP). This tutorial includes the generation of ligand parameters using OPLS, how to prepare a protein system, and how to run ligand and protein FEP calculations. These examples are based on ligand binding of CDk2 inhibitors.
-
Install a working version of Q, e.g.:
-
Clone this repository:
git clone https://github.com/qusers/qligfep.git
-
Create the shipped conda environment
conda env create -f environment.yml
In settings.py:
-
Change SCHROD_DIR to the Schrodinger location, if you want to be able to generate OPLS ligand parameters using ffld_server.
-
Change Q_DIR to the location of the q executables. This can be particularly useful if you use setupFEP from a local machine on a mounted directory. (In which case, the executables of the preparation part and running part of Q are at several places).
-
You can add slurm specific parameters in the CLUSTER INPUTS section, according to the given example.
- ffld_server
- cgenff
- Protein Preparation Wizard
- Python3.10
- Q
contact: Willem Jespers (PhD)