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QligFEP v2.0 and QresFEP v1.0

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 two main modules:

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 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.

Installing QligFEP and QresFEP

  • Install a working version of Q, e.g.:

https://github.com/esguerra/Q6

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.

Requirements

  • ffld_server
  • cgenff
  • Protein Preparation Wizard
  • Python2.7.XX
  • Q

contact:willem.jespers@icm.uu.se

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