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 Sire, AMBER (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.
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