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. It includes modules which are described in further detail below:
- setupFEP.py: module to generate ligand FEP calculations using a dual topology approach, see Jespers et al. (doi:/MS_SUBMITTED).
- resFEP.py: module to setup protein FEP calcultions, based on Boukharta et al. (https://doi.org/10.1371/journal.pcbi.1003585) and Jespers et al. (see doi://MS_SUBMITTED).
- protprep.py: a module to prepare proteins for simulations under spherical boundary conditions.
- opls2Q and charmm2Q.py: tools to translate from OPLS (ffld_server) and CHARMM (cgenff) to Q readable file formats.
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. (resFEP/ligFEP). 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, and protein stability calculations on T4-lysozyme. Each topic is stored within a seperate folder, and includes a README file including a step by step description of the protocol.
- Install a working version of Q, e.g.:
https://github.com/esguerra/Q6
- Clone this repository:
git clone https://github.com/jesperswillem/setupFEP.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.
- ffld_server
- cgenff
- Protein Preperation Wizard
- Python2.7.XX
- Q