FESetup: Automating Setup for Alchemical Free Energy Simulations

Hannes H Loeffler; Julien Michel; Christopher Woods

doi:10.1021/acs.jcim.5b00368

FESetup: Automating Setup for Alchemical Free Energy Simulations

Hannes H Loeffler, Julien Michel, Christopher Woods

School of Chemistry

Research output: Contribution to journal › Article › peer-review

Abstract / Description of output

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 language	English
Pages (from-to)	2485-90
Number of pages	6
Journal	Journal of Chemical Information and Modeling
Volume	55
Issue number	12
DOIs	https://doi.org/10.1021/acs.jcim.5b00368
Publication status	Published - 28 Dec 2015

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http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00368

Cite this

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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.",

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FESetup: Automating Setup for Alchemical Free Energy Simulations

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