FESetup FESetup
(7 votes)

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

Support: A mailing list for user support can be subscribed to here.



The code is written in Python 2.7 with main dependencies on AmberTools, Sire, Openbabel and RDKit.

Version 1.2.1
(7 votes)
MD5 Checksum 63d2d6f4a823df4e3250a5ea6e58b74a
Downloads 3,739
Author Hannes Loeffler
License GNU/GPL external
SHA1 Checksum 4610de701f99bd702724d84f7e9265a61b1be3ad