title: FESetup: Automating Setup for Alchemical Free Energy Simulations.
abstract: FESetup is a new pipeline tool which can be used flexibly within larger workflows. The tool aims to support fast and easy setup of alchemical free energy simulations for molecular simulation packages such as AMBER, GROMACS, Sire, or NAMD. Post-processing methods like MM-PBSA and LIE can be set up as well. Ligands are automatically parametrized with AM1-BCC, and atom mappings for a single topology description are computed with a maximum common substructure search (MCSS) algorithm. An abstract molecular dynamics (MD) engine can be used for equilibration prior to free energy setup or standalone. Currently, all modern AMBER force fields are supported. Ease of use, robustness of the code, and automation where it is feasible are the main development goals. The project follows an open development model, and we welcome contributions.
authors.affiliation: Scientific Computing Department, STFC Daresbury , Keckwick Lane, Warrington WA4 4AD, United Kingdom.
authors.forename: Hannes H
authors.initials: HH
authors.lastname: Loeffler
authors.affiliation: EaStCHEM School of Chemistry, University of Edinburgh , West Mains Road, Edinburgh EH9 3JJ, United Kingdom.
authors.forename: Julien
authors.initials: J
authors.lastname: Michel
authors.affiliation: BrisSynBio, University of Bristol , 8-10 Berkeley Square, Bristol BS8 1HH, United Kingdom.
authors.forename: Christopher
authors.initials: C
authors.lastname: Woods
mesh_terms: D003198:Computer Simulation; D008024:Ligands; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D013816:Thermodynamics
chemical_list: D008024:Ligands