This collection of python command line functions is designed with the aim to faciliate 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 pacakge includes at the moment four main modules:
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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).
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QresFEP.py: module to generate protein FEP calculations using either a single topology approach, see Jespers et al. (https://doi.org/10.1021/acs.jctc.9b00538), or using a dual topology approach, see Koenekoop et al. (https://doi.org/10.1038/s42004-025-01771-0).
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QLIE.py: module to generate ligand LIE calculations.
Future versions will include 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 faciliate high throughput setup. Additionally, a tutorials folder is included, with one tutorial showing a detailed description of the setup procedure for ligand mutations as published in Jespers et al. (QligFEP). This tutorial includes the generation of ligand parameters using OPLS, how to prepare a protein system, and how to run ligand FEP calculations. These examples are based on ligand binding of CDK2 inhibitors. Another tutorial shows a detailed description of the setup procedure for residue mutations as published in Koenekoop et al. (QresFEP). This tutorial includes the generation of mutant amino acids, how to prepare a protein system, and how to run residue FEP calculations. These examples are based on thermal stability shifts of T4L mutants.
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Install a working version of Q, e.g.: https://github.com/esguerra/Q6
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Clone this repository:
git clone https://github.com/qusers/qligfep.git -
Initialize the repository:
bash qligfep_init.shThis will add qligfep repo executables to your $PATH and update the settings.py script with:
- Q_PATH: the path to your Q installation
- SCHROD: the path to your Schrödinger installation
- DEFAULT: your working HPC cluster (or localhost)
You can modify you setting.py script further manually to add more clusters or cluster options.
Schrödinger
- PyMOL
- Protein Preparation Wizard
- ffld_server
Software
- Q
- cgenff
- Python3.XX
Python packages
- mdtraj
contact: w.jespers@rug.nl