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Comparison of gmx_MMPBSA vs other programs

This comparison is based on the documentation of the different programs

Calculation features

Feature g_mmpbsa GMXPBSA 2.1 MMPBSA.py 1 gmx_MMPBSA
Normal binding free energies PB PB PB 10 and GB PB 10 and GB
* GB models 1, 2, 5, 7 and 8 1, 2, 5, 7, 8 and NSR6
Stability
Alanine scanning 2
Entropy corrections 3 NMODE and QH NMODE, QH, IE, and C2
Decomposition schemes Per-Residues Per-Residues and Per-Wise Per-Residues and Per-Wise
QM/MMGBSA
MM/3D-RISM
Support Membrane Protein
Approximations ST ST and MT ST and MT ST and MT

Analysis features

Feature g_mmpbsa GMXPBSA 2.1 MMPBSA.py 1 gmx_MMPBSA
API
Analyzer Tool 4
* Multiple systems at same time
* Correlation between systems
* Per-residue energies to PDB
* Interactive visualization
** 3D Molecular Visualization PyMOL
** Interactive Charts static image
* Plotting tool internal tools API and graphics library 5 gmx_MMPBSA_ana
* Energetic Terms charts ΔGpolar, ΔGnonpolar, ΔEMM and ΔGbind All
* Export data to CSV file
** Energy Summary
** Individual Energetic Terms

Technical features

Feature g_mmpbsa GMXPBSA 2.1 MMPBSA.py 1 gmx_MMPBSA
GROMACS Version 4.x, 5.x and 2016+ 6 4.x, 5.x and 20xx.x 7 --- 4.x, 5.x and 20xx.x
Dependencies APBS (1.2.x, 1.3.x or 1.4.x) APBS (1.x.x) 8 AmberTools20/21 AmberTools20/21 9
Parallel computation Depends on APBS Locally using APBS or in HPC divided in jobs
Steps for:
* Calculation and Summary Multiple Multiple One One
* Analysis Multiple Multiple Multiple One

  1. MMPBSA.py is included in AMBER package ↩↩↩

  2. Without documentation ↩

  3. NMODE = Normal modes approximation, QH = Quasic-Harmony approximation, IE = Interaction Entropy approximation, and C2 = C2 Entropy ↩

  4. We plan to extend gmx_MMPBSA compatibility to MMPBSA.py's results ↩

  5. Currently there is a repository (AmberUtils) for analysing the results ↩

  6. GROMACS 20xx.x is not officially supported. There is a Pull Request that offers a minimum compatibility with versions higher than 2016.x one, but still with limitations ↩

  7. It is not clear whether it does support GROMACS versions 20xx.x or not, but we assume that it does since it is script-based ↩

  8. It is not clear whether it does support APBS versions 3.x.x ↩

  9. gmx_MMPBSA is compatible with AmberTools20, AmberTools21, and AmberTools22 ↩

  10. gmx_MMPBSA supports Linear and Non-Linear PB equations. MMPBSA.py on the other hand, requires the user to modify manually the *.mdin input files ↩↩

Last update: June 8, 2022 23:48:53
Created: February 8, 2021 07:10:13
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