gxm_MMPBSA v1.3.1 (09/02/2021)

Additions

• New variable (overwrite_data) to overwrite gmx_MMPBSA data.
• More informative message when sander fail. Useful for PB calculation

Fixes

• Protein-ligand with charmm force field example
• Stability calculation
• gmx path error
• leaprc.GLYCAM_06h-1 file
• Protein-glycan example

Changes

• Documentation banner

gxm_MMPBSA v1.3.0 (08/02/2021)

Additions

• Documentation at Github pages
• Charmm force field support
• Amber topology generation from GROMACS topology. Work for Charmm and Amber force fields
  • New flag for topologies (-cp, -rp and -lp) added
• Now gmx_MMPBSA supports discontinuous receptor and ligand.
• Glycine scanning
• Autocompletion script for both gmx_MMPBSA and gmx_MMPBSA_ana
• Versioneer to control the semantic version.
• Argument type checker for the command-line

Fixes

• Alanine scanning tutorial
• GROMACS executable path
• The -gui option has been changed by -nogui and fixed when it is defined
• Improvement on documentation

Changes

• Documentation theme. Now we use Material
• Alanine scanning variable. Now mutant correspond to mutant amino acid (ALA and GLY)
• The gmx_MMPBSA_gui was changed by gmx_MMPBSA_ana
• Improvement on the topologies construction process
• Order in which the trajectories are cleaned. Now, the topology is built and finally, the trajectories are cleaned

gmx_MMPBSA v1.2.0

Improvements

• More comprehensive output log file
• Best handling of structure files

Additions

• New ligand force field (Zwitterionic aminoacids)
• A new flag (-cr) added for defining a reference structure (guarantee a better consintency in generated PDB files)
• API documentation

Changes

• gmx editconf is used to generate PDB files instead of gmx trjconv (#14)
• gmx_MMPBSA data is copied in AMBER as an independent folder
• *gro files can be used as a MD Structure+mass(db) file
• Updated tutorial list in README (Protein_DNA_RNA_Ion_ligand BFE calculations)

gmx_MMPBSA v1.1.1

• Support various metallo-complexes formats
• New tutorial added (see Protein_DNA_RNA_Ion_ligand tutorial)
• Keep all the temporary files in the folder for debugging purposes

gxm_MMPBSA v.1.1.0

In this version, we have changed and implemented several functions:

• Now supports carbohydrates as ligand. See this tutorial
• Now supports metalloprotein-ligand complexes. See this tutorial. (it has limitations, see issue)
• We changed the notation of the force fields, now the user can define any force field (We have only tested Amber and GLYCAM force fields) available in AmberTools. Charmm is not yet supported. See this section
• We have added data folder to gmx_MMPBSA module. This folder contains the GLYCAM_06h-1 force field files (Compatible with amber99sb and early, see at http://glycam.org) which is not in AmberTools.

gxm_MMPBSA first release

gmx_MMPBSA is a new tool aid to perform end-state free energy calculations based on AMBER's MMPBSA.py with GROMACS files.
This version includes:

• Compatibility with different Gromacs versions
• Support for all types of calculations available in MMPBSA.py
• Graphical user interface for results analysis (gmx_MMPBSA_gui)
• API modified to get more information
• Some new facilities and types of calculations

Consult the documentation for more information

New features to implement:
gmx_MMPBSA_gui

• Add tooltips for more information
• Add detailed documentation
• Add customization options for graphics
  • Labels, titles, rotation, color, etc
  • Selection of intervals for calculations
  • Option to visualize several types of calculations in the same graph
• Add new menu with documentation, about, version, and check updates

API

• documentation
• incorporate Interaction Entropy