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:

• 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_single.py: module to generate protein FEP calculations using a single topology approach, see Jespers et al. (https://doi.org/10.1021/acs.jctc.9b00538).

• QresFEP_dual.py: module to generate protein FEP calculations using a dual topology approach.

• QLIE.py: module to generate ligand LIE calculations.

Future versions will 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 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.:

https://github.com/esguerra/Q6

• Clone this repository:

  git clone https://github.com/qusers/qligfep.git

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 preperation 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.

Schrödinger

• Protein Preparation Wizard
• ffld_server Software
• Q
• cgenff
• Python3.XX Python packages
• mdtraj

contact:[email protected]