Getting started
gmx_MMPBSA is a tool based on AMBER's MMPBSA.py that performs end-state free energy calculations using GROMACS files. It supports a broad range of GROMACS versions and improves compatibility, versatility, analysis, and parallelization compared with existing programs (see the detailed comparison).
Cite gmx_MMPBSA
The official gmx_MMPBSA paper was published in the Journal of Chemical Theory and Computation and is available here. If you use gmx_MMPBSA, please cite it as follows:
Valdés-Tresanco, M.S., Valdés-Tresanco, M.E., Valiente, P.A., and Moreno, E. gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS. Journal of Chemical Theory and Computation, 2021 17 (10), 6281-6291. https://pubs.acs.org/doi/10.1021/acs.jctc.1c00645.
Please also consider citing the MMPBSA.py paper:
Bill R. Miller, T. Dwight McGee, Jason M. Swails, Nadine Homeyer, Holger Gohlke, and Adrian E. Roitberg. MMPBSA.py: An Efficient Program for End-State Free Energy Calculations. Journal of Chemical Theory and Computation, 2012 8 (9), 3314-3321. https://pubs.acs.org/doi/10.1021/ct300418h.
Download | *.bib | *.ris | *.xml
Visit the Cite gmx_MMPBSA page for more information on how to cite gmx_MMPBSA and the programs/methods implemented in it.
Installation¶
Ready to use gmx_MMPBSA 😀? See the installation page.
What can be done with gmx_MMPBSA?¶
Multiple calculations can be performed with gmx_MMPBSA, such as:
- Binding free energy calculations with PB, GB and/or 3D-RISM models
- Alanine scanning
- Binding free energy decomposition
- Entropy corrections (IE, C2, NMODE)
- Stability
- QM/MMGBSA
There is always more...
You can check gmx_MMPBSA in a nutshell page for a more detailed overview of the types of calculations supported in gmx_MMPBSA. Also, check our example page to see a detailed list of all the examples available.
In the current version, gmx_MMPBSA supports a number of different systems, including but not limited to:
- Protein-protein
- Protein-ligand
- Protein-DNA
- Metalloprotein-ligand
- Protein-glycan
- Membrane proteins
- Multicomponent system (Comp_receptor)
Supported input and force-field workflows
The 1.7.0 release includes tested conversion paths for representative Amber, OPLS, and CHARMM GROMACS topologies, plus a native-AMBER entry point and a PSF/DCD example. This does not mean that every system built by pdb2gmx, CHARMM-GUI, NAMD, or another package is validated automatically. Topology completeness, conversion limitations such as omitted CHARMM CMAP terms (relevant mainly for MTP; they cancel under STP), the selected implicit-solvent model, and the trajectory protocol still determine whether a calculation is scientifically appropriate. See the compatibility guide and the example page for tested representatives and known restrictions.
The following video shows how to perform a typical binding free energy calculation with the GB model and the interaction entropy method in gmx_MMPBSA.
A quick overview of gmx_MMPBSA¶
gmx_MMPBSA is a Python module that contains four applications:
- gmx_MMPBSA is the main application and carries out the calculations mentioned above
- amber_MMPBSA runs supported native-AMBER topology/trajectory/mask workflows without GROMACS input files
- gmx_MMPBSA_ana provides an intuitive way to analyze the data from gmx_MMPBSA calculations and save high-quality pictures
- gmx_MMPBSA_test tests whether the installation was successful by running one or more available examples in gmx_MMPBSA.
The native-AMBER command supports ST and MT workflows where applicable; explicit-water and MT entropy restrictions are described in the native-AMBER guide.
Easy to run
gmx_MMPBSA can run in parallel and requires only a few things to perform any calculation. That is:
- an input parameters file (
*.in, contains all the specifications regarding the type of calculation that is going to be performed) - a MD Structure+mass(db) file (
*.tpr,*.pdb) - an index file (
*.ndx) - receptor and ligand groups (group numbers or names in the index file)
- a trajectory file (
*.xtc,*.pdb,*.trr) - a topology file (
*.top) — required; parameters are converted from the GROMACS topology (-cp)
After the calculation, results can be analyzed with gmx_MMPBSA_ana.
See How gmx_MMPBSA works for more details. The examples page shows how gmx_MMPBSA works with real systems.
If you prefer a more general overview of the gmx_MMPBSA suite, check this amazing video by Dr. Hymavathi Veeravarapu.
Need help?¶
The help section contains answers to frequently asked questions and common errors. You can also search our Google group or the issues for similar cases.
If you still have questions or cannot solve the problem, please consider opening an issue or posting in our Google group
Follow gmx_MMPBSA¶
Visit Pypi Stats or PePy to see the latest stats for gmx_MMPBSA.
Acknowledgments¶
- First of all, to Amber and GROMACS developers. Without their incredible and hard work, gmx_MMPBSA would not exist.
- Jason Swails (Amber developer and ParmEd principal developer) for his continuous support on ParmEd issues.
- Dr. Hymavathi Veeravarapu for helping with the introductory video for gmx_MMPBSA
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To the Open Source license of the JetBrains programs.
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To all researchers who help improve gmx_MMPBSA with comments, feedback, and bug reports.
Created: February 8, 2021 07:10:13