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Examples

Here you can find a representation of almost all the types of calculations and analyses that you can perform with gmx_MMPBSA. Although each example focuses on specific cases, you can use gmx_MMPBSA on systems that combine a number of different components (i.e. metalloprotein-ligand complex, Protein-DNA-ligand, etc.). In addition, several types of calculations (e.g. GB, Alanine scanning and Per-residue decomposition; PB, Interaction Entropy, and Per-wise decomposition) can be also performed in the same run for a specific system.

Systems

This is a representation of the systems that can be processed and analyzed with gmx_MMPBSA. Our program has a robust method to process input structures. Even if your system is not represented here, still have a go, you won't be disappointed! 😀

CHARMMff support

This section focuses more on how to work with systems prepared with CHARMM force fields. We only show few examples for better clarity.

OPLSff support

This section focuses more on how to work with systems prepared with OPLS force fields. We only show few examples for better clarity.

Analysis

This section focuses on the analysis that can be performed with gmx_MMPBSA. Although each example focuses on specific cases, you can use gmx_MMPBSA to perform several types of calculations (e.g. GB, Alanine scanning and Per-residue decomposition; PB, Interaction Entropy, and Per-residue decomposition) in the same run for a specific system.

Support for psf_dcd files

This section focuses on how to work with psf-dcd files. These files are used for several MD simulation programs such as NAMD, OpenMM or GENESIS. We plan to add more examples in the near future.


  1. It is part of the All set defined with -t 0 in gmx_MMPBSA_test 

  2. It is part of the Minimal set defined with -t 1 in gmx_MMPBSA_test 

  3. It is part of the Fast set defined with -t 2 in gmx_MMPBSA_test 


Last update: June 10, 2022 21:50:33
Created: November 9, 2020 14:28:26
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