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Gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS

dc.contributor.authorValdés-Tresanco M.S
dc.contributor.authorValdés-Tresanco M.E
dc.contributor.authorValiente P.A
dc.contributor.authorMoreno E.
dc.date.accessioned2022-09-14T14:33:47Z
dc.date.available2022-09-14T14:33:47Z
dc.date.created2021
dc.identifier.issn15499618
dc.identifier.urihttp://hdl.handle.net/11407/7472
dc.descriptionMolecular mechanics/Poisson-Boltzmann (Generalized-Born) surface area is one of the most popular methods to estimate binding free energies. This method has been proven to balance accuracy and computational efficiency, especially when dealing with large systems. As a result of its popularity, several programs have been developed for performing MM/PB(GB)SA calculations within the GROMACS community. These programs, however, present several limitations. Here we present gmx_MMPBSA, a new tool to perform end-state free energy calculations from GROMACS molecular dynamics trajectories. gmx_MMPBSA provides the user with several options, including binding free energy calculations with different solvation models (PB, GB, or 3D-RISM), stability calculations, computational alanine scanning, entropy corrections, and binding free energy decomposition. Noteworthy, several promising methodologies to calculate relative binding free energies such as alanine scanning with variable dielectric constant and interaction entropy have also been implemented in gmx_MMPBSA. Two additional tools - gmx_MMPBSA_test and gmx_MMPBSA_ana - have been integrated within gmx_MMPBSA to improve its usability. Multiple illustrating examples can be accessed through gmx_MMPBSA_test, while gmx_MMPBSA_ana provides fast, easy, and efficient access to different graphics plotted from gmx_MMPBSA output files. The latest version (v1.4.3, 26/05/2021) is available free of charge (documentation, test files, and tutorials included) at https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA. ©eng
dc.language.isoeng
dc.publisherAmerican Chemical Society
dc.relation.isversionofhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85117187011&doi=10.1021%2facs.jctc.1c00645&partnerID=40&md5=05824675e3fc89747f3f6fe9017c6406
dc.sourceJournal of Chemical Theory and Computation
dc.titleGmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS
dc.typeArticle
dc.rights.accessrightsinfo:eu-repo/semantics/restrictedAccess
dc.publisher.programCiencias Básicas
dc.type.spaArtículo
dc.identifier.doi10.1021/acs.jctc.1c00645
dc.publisher.facultyFacultad de Ciencias Básicas
dc.affiliationValdés-Tresanco, M.S., Faculty of Basic Sciences, University of Medellin, Medellin, 050026, Colombia
dc.affiliationValdés-Tresanco, M.E., Centre for Molecular Simulations, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
dc.affiliationValiente, P.A., Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada, Center of Protein Studies, Faculty of Biology, University of Havana, 25 & J, La Habana, 10400, Cuba
dc.affiliationMoreno, E., Faculty of Basic Sciences, University of Medellin, Medellin, 050026, Colombia
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dc.type.versioninfo:eu-repo/semantics/publishedVersion
dc.type.driverinfo:eu-repo/semantics/article
dc.identifier.reponamereponame:Repositorio Institucional Universidad de Medellín
dc.identifier.repourlrepourl:https://repository.udem.edu.co/
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