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Mario Sergio Valdés Tresanco, Mario E. Valdés‐Tresanco, Mario E. Valdés-Tresanco, Mario E. Valdés-Tresanco, Pedro Alberto Valiente, Ernesto Moreno
Molecular 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.
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Tresanco, M. S. V., Valdés‐Tresanco, M. E., Valdés-Tresanco, M. E., Valdés-Tresanco, M. E., Valiente, P. A., & Moreno, E. (2021). gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS. Journal of Chemical Theory and Computation, 17(10), 6281–6291. https://doi.org/10.1021/acs.jctc.1c00645
Tresanco, Mario Sergio Valdés, et al. "gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS." Journal of Chemical Theory and Computation, vol. 17, no. 10, 2021, pp. 6281–6291, https://doi.org/10.1021/acs.jctc.1c00645.
Tresanco, Mario Sergio Valdés, Mario E. Valdés‐Tresanco, Mario E. Valdés-Tresanco, Mario E. Valdés-Tresanco, Pedro Alberto Valiente, and Ernesto Moreno. "gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS." Journal of Chemical Theory and Computation 17, no. 10 (2021): 6281–6291. https://doi.org/10.1021/acs.jctc.1c00645.
Tresanco M. S. V., Valdés‐Tresanco M. E., Valdés-Tresanco M. E. [и др.] gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS // Journal of Chemical Theory and Computation. — 2021. — Vol. 17, № 10. — P. 6281–6291. — URL: https://doi.org/10.1021/acs.jctc.1c00645
@article{tresanco2021gmxmmpbsa,
title = {{gmx\_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS}},
author = {Mario Sergio Valdés Tresanco and Mario E. Valdés‐Tresanco and Mario E. Valdés-Tresanco and Mario E. Valdés-Tresanco and Pedro Alberto Valiente and Ernesto Moreno},
journal = {Journal of Chemical Theory and Computation},
year = {2021},
volume = {17},
number = {10},
pages = {6281--6291},
doi = {10.1021/acs.jctc.1c00645},
url = {https://doi.org/10.1021/acs.jctc.1c00645}
}TY - JOUR AU - Tresanco, Mario Sergio Valdés AU - Valdés‐Tresanco, Mario E. AU - Valdés-Tresanco, Mario E. AU - Valdés-Tresanco, Mario E. AU - Valiente, Pedro Alberto AU - Moreno, Ernesto TI - gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS JO - Journal of Chemical Theory and Computation VL - 17 IS - 10 SP - 6281 EP - 6291 PY - 2021 DA - 2021/09/29 DO - 10.1021/acs.jctc.1c00645 UR - https://doi.org/10.1021/acs.jctc.1c00645 ER -
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