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:
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setupFEP.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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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.
- Install a working version of Q, e.g.:
https://github.com/esguerra/Q6
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Clone this repository:
In settings.py:
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Change SCHROD_DIR to the Schrodinger location, if you want to be able to generate OPLS ligand parameters using ffld_server.
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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).
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You can add slurm specific parameters in the CLUSTER INPUTS section, according to the given example.
- ffld_server
- cgenff
- Protein Preparation Wizard
- Python2.7.XX
- Q
contact:willem.jespers@icm.uu.se