QligFEP v2.0 and QresFEP v1.0

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.

Installing QligFEP and QresFEP

• Install a working version of Q, for example:

  https://github.com/qusers/Q6

• Clone this repository:

  git clone https://github.com/manuel-orozco/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.

Requirements

• ffld_server
• cgenff
• Protein Preparation Wizard (Schrodinger Maestro)
• Python3.10
• Q

You can download a free, academic version of Schrodinger Maestro here: https://www.schrodinger.com/freemaestro

contact: [Manuel Orozco (PhD)]