FESetup FESetup 1.2

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FESetup is a tool to automate the setup of alchemical free energy (AFE) simulations like thermodynamic integration (TI) and free energy perturbation (FEP). Post–processing methods like MM–PBSA and LIE are supported too.  FESetup can also be used for general simulation setup ("equilibration") through an abstract MD engine.  Mapping of corresponding atoms between the two free energy states of a relative AFE simulation can be computed via a maximum common substructure search (MCSS).  This enables a maximal single topology description of the perturbed molecule pair.  Ligand molecules are automatically parameterised using the AMBER GAFF/AM1-BCC method.

The supported free energy simulation packages are currently SireAMBER (sander/pmemd), GROMACS and CHARMM/PERT.  All these codes implement AFE simulation by making use of a hybrid single/dual topology description of the perturbed region. There is also some support for NAMD's dual topology feature but this requires an additional PDB file to designate appearing/vanishing atoms and relative restraints to keep ligands spatially together.

General simulation setup through an abstract MD engine is available for AMBER, GROMACS, NAMD and DL_POLY. Supported force fields are all modern AMBER force fields including GAFF for small organic molecules.

Citation: A detailled description has been published in DOI: 10.1021/acs.jcim.5b00368. Please cite this when you use FESetup.

 

How FESetup works

 

Future plans include extending the code to support other popular biomolecular simulation software, additional force fields and parameterisation schemes. We particularly aim at automatisation where it makes sense and is possible, ease of use and robustness of the code.

The basis of the current code was a collection of Python and shell scripts written previously by Julien Michel and Christopher Woods. The current code base is now mainly developed by Hannes Loeffler with contributions from the original developers. The code is written in Python 2.7 with main dependencies on AmberTools, Sire, Openbabel and RDKit.

 

Reference/Citation:

Please cite DOI: 10.1021/acs.jcim.5b00368.

 

Tutorial Files
(see Documentation below for background information on these tutorials)

First Impressions: an introductory tutorial which the main emphasis on key features of FESetup and also a basic test case.

T4 lysozyme: setup of multiple protein structures and free energy simulations of a complex.

 

Documentation

User documentation including installation notes and tutorials to get started.

 

Support

discussion board about FESetup and related topics.

 

Mailing List

For up to date information and announcements, a mailing list can be subscribed to here.

Version  1.2  Downloads  1,477 
Size  91.3 MB  License GNU/GPL external
Author Hannes Loeffler external Website
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