FESetup: Automating Setup for Alchemical Free Energy Simulations

Hannes H Loeffler, Julien Michel, Christopher Woods

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Pages (from-to)2485-90
Number of pages6
JournalJournal of Chemical Information and Modeling
Volume55
Issue number12
DOIs
Publication statusPublished - 28 Dec 2015

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