gmx_MMPBSA v1.5.0.2 (02/24/2022)

What's Changed

• Improve topology cleanup #165

Full Changelog: v1.5.0.1...v1.5.0.2

gmx_MMPBSA v1.5.0.1 (02/22/2022)

Fixes

gmx_MMPBSA

• Allow index group name for group selection (#157)

gmx_MMPBSA_ana

• gmx_MMPBSA_ana does not open at the end of the calculation (#158)

gmx_MMPBSA v1.5.0 (02/22/2022)

Additions

gmx_MMPBSA

• Support for all files generated with CHARMM-GUI for Amber force fields (ff14SB and ff19SB)
• enabled NonLinear PB solver in sander (#63)
• enabled all pbsa options in sander (#64)
• enabled all 3D-RISM variables (#68)
• Improve IE output data (#91)
• New C2 Entropy method added (#73)
• Option to create an input file (--create_input)
• New format file (h5) to store all the data result (Experimental)
• New method to get the decomp data without the API classes
• Report energy differences for every term in alanine scanning
• Automatic calculation of charge for com , rec, and lig groups in QM/MMGBSA
• Improve residue selection in QM/MMGBSA
• New modified PB Radii sets for GAFF (#140) and CHARMM (#141) force fields
• conda package (#55)
• Checking structure consistency method (#44)

gmx_MMPBSA_ana

• Chart properties selector. The following properties can be changed:
  • Font size:
    • Axes (Ticks, Labels)
    • Title, Subtitle and legend
    • Color bar
  • Pallete, color or theme:
    • Line plot
    • Bar plot
    • Heatmap plot
    • PyMOL visualization
  • Rotation, padding and number of ticks
  • Figure size, dpi and format
  • Chart type specific properties
  • Highlight or split components
• Frame range and interval selection
• Chart data can be visualized in table format and copy directly to excel
• Summary table for complex, receptor, ligand, etc.
• Now the outputs files can be visualized as document in their own sub-window
• New button to launch all the graphics and functions associated to item
• Highlighted Bar and Heatmap plot
• User setting file per-system
• Frames to Time conversion

Documentation

• Code block names and annotations

Fixes

gmx_MMPBSA

• Protonated residues (#42)
• Inconsistent energy between tleap and ParmEd topology (#147)
• Error with alphanumeric residue numbers (#134)
• print_res selection scheme
• Error when startframe=0 (#66)
• parmchk2 always uses GAFF as force field (#45)
• IE is calculated for PB and GB independently (#72)
• Alanine scanning with CHARMM ff (#88)
• MT approach (#78)
• get_num_terms function run forever if TDC term not found. (#98)
• Check if the groups defined for receptor and ligand are the same (#86)
• Add SD and SEM calculated with propagation formula (#105)
• Structure consistency (#80, #79)
• gmx_MMPBSA launches an error when there is an OverflowError on IE calculation (#57)
• Improve gmx_MMPBSA.log file (#108)
• Inconsistency with multiple trajectories (#120)
• Alanine Scanning ERROR on THR to ALA mutation (#139)

gmx_MMPBSA_ana

• Tick labels in line plots (#65)
• Improved PyMOL 3D visualization (#85)
• Improved the system options in the init dialog

gmx_MMPBSA_test

• Error when -f option it not defined (#46)

Changes

gmx_MMPBSA

• Recalculate the PB energy with --rewrite-output changing the value of inp (#144)
• Removed deprecated variables
• Input file format. Although it kept the structure of the previous version, the current one is more GROMACS alike
• EnergyVector changed to ndarray subclass
• Regen expression for mutant_res
• Now the COM, REC and LIG trajectories must have the same length when using MT approach
• Improve verbose logging in gmx_MMPBSA.log file (#108)
• Removed *.gro file support in -cs , -rs and -ls flags
• Added trjconv to avoid the PBC in the tpr file (#43)

gmx_MMPBSA_ana

• New set of chart buttons
• IE plot

gmx_MMPBSA_test

• Improved parallel processing
• Change command-line

Documentation

• Updated packages dependency
• Input and Output file pages

gmx_MMPBSA v1.4.3 (26/05/2021)

Additions

• Added two new tutorials Protein_ligand_LPH_atoms_CHARMMff and QM/MMGBSA calculations
• Now the program reports the p-value associated with the correlation coefficient when performing the correlation analysis
• Google Analytics is used as a third-party tracking service to improve documentation. Check our Private Policy for more details

Fixes

• Minor fixes in the documentation
• Improved parsing of forcefields variable
• Fixed bug when gmx_MMPBSA_ana runs without arguments
• Fixed compatibility with older files (< v1.4.0)
• Fixed error when debug_printlevel > 1 in tleap command

Changes

• Now the command line used is added to the log file
• The gmx_MMPBSA data folder is exported directly rather than copied in the $AMBERHOME data folder.

gmx_MMPBSA v1.4.2 (02/05/2021)

Additions

• Added Covid-19 and other complex systems as examples in the documentation
• Added Q&A section to the documentation
• Implemented an adaptive intdiel(GB)/indi(PB) for Alanine scanning (Check the input file section)

Fixes

• Fixed bug when startframe = 0 (#33)
• Fixed bug when blank lines exist in [molecule] section in topology file
• Fixed pipe command-line for Gromacs execution in macOS
• Fixed compatibility issues with v1.3.x
• Improved and fixed the documentation
• Improved output file information related to ΔG binding
• Improved calculation with different entropy approximations simultaneously

Changes

• Changed protein_forcefields and ligand_forcefield by forcefields variable in all examples
• Now QH and IE can be calculated at the same time
• entropy variable was separated in qh_entropy and interaction_entropy. The entropy variable is deprecated
  and will be removed in the next major version (v1.5.0).
• entropy_seg was replaced by ie_segment. The entropy_seg variable is deprecated and will be removed in the
  next major version (v1.5.0).

gmx_MMPBSA v1.4.1 (08/04/2021)

Additions

• New class Residue added to handle residues selection in Gromacs format with Amber index
• Verification of the presence of water molecules in receptor and ligand groups
• Gromacs timer added

Fixes

• Gromacs topology conversion
• qm_residues notation
• Default path in gmx_MMPBSA_test
• The Entropy representation in gmx_MMPBSA_ana
• Bug when the structure has insertion code
• Improved ΔG Binding plot representation

Changes

• Now forcefields variable unifies protein_forcefield and ligand_forcefield. These variables protein_forcefield
  and ligand_forcefield are deprecated and will be removed in the next major version (v1.5.0).
• Improved documentation
  • Examples
  • Command-line
    • MPI
    • Examples
  • Links and references
  • Updated to material 7.1.0
    • Dark mode
    • Material "Back to Top" button
    • Grammatical corrections
  • Installation section
  • Figures caption
• The Ambiguous name for Entropy term in output files

gmx_MMPBSA v1.4.0 (22/03/2021)

This release focuses almost entirely on gmx_MMPBSA_ana with minor issues fixed in gmx_MMPBSA

Additions

• New start window to select options
  • Option to make correlation (Pearson and Spearman coefficients)
  • Option to hide decomposition data
  • Option to not compute charts with a non-significant contribution
  • Option to not include terms with a non-significant contribution in bar charts
  • Selection of the components to display in addition to Delta (i.e. complex, receptor, and ligand)
  • Toggle the chart toolbar for a cleaner visualization
  • An informative table with selected systems data
    • Option to exclude any system
    • Option to change:
      • The system name
      • The experimental Ki for correlation
      • The temperature to calculate the Experimental Energy and the Interaction Entropy
  • Data reader with progress bar and multiprocessing
• Multiple systems to analyze in the same session
• Correlation dock
  • Multiple models at the same time
  • Graphs and correlation data for each calculated energy term (ΔH, ΔH+IE, ΔH+NMODE and ΔH+QH)
  • Table with the experimental energy of the systems, and the data of the selected model
• New arguments flags for gmx_MMPBSA_ana (See the gmx_MMPBSA_ana documentation)
  • replaced -p by -f
  • -f accept a folder, single info file or a list of them
  • New flag -r. This flag allows to load all the systems inside a selected folder
• New graphical options
  • A new set of graphics (heatmap)
    • Per-frame when analyzing Per-residue and pair in Per-wise
    • Relation matrix for Per-wise
  • Interactive visualization of PDB files with per-residue energies with PyMOL (up to 5 instances).
  • Regression plot for correlation
• Plot features
  • Added Standard deviation to bar plots
  • Added rolling average to line plots
  • Added indicators for the selected interval and average value in IE chart
  • Added crosshair cursor for better analysis on charts
• Multiprocessing application for testing (gmx_MMPBSA_test)
• Embed Youtube videos for gmx_MMPBSA_ana

Fixes

• Now gmx_MMPBSA_ana shows stability results as expected
• Errors in the documentation
• MPI

Changes

• Converted analyzer.py into a sub-module for more flexibility, organization and portability
• Residues notation for mutation: CHAIN:RESNAME:RESNUMBER:ICODE instead of Amber residue index
• Improve the selection method in decomposition calculation
• Replaced variable entropy_temp (deprecated) by temperature
• IE in API
• Color Palette used in graphs
• Use seaborn and matplotlib for charts
• Use Pandas Dataframe and numpy to store data
• Changed the data structure to implement dynamic selection of frames in future versions
• Improved data export: now any item can be exported as CSV file
• Improved the documentation
  • Improve examples documentation
  • Added changelog button at home
  • Separated changelog in a new header
  • Added tags to mark the history of changes of variables and functionalities

gmx_MMPBSA v1.3.3 (10/03/2021)

Fixes¶

• fixed Boltzmann constant for IE
• fix the ligand mutation
• fixed analyzer error when interval > 1
• fixed residue selection within
• fixed ChainID assignation when no reference structure is defined
• fixed the selection to print when decomposition

gxm_MMPBSA v1.3.2 (01/03/2021)

Additions

• Now, gmx_MMPBSA is in Zenodo . You can refer to us in this way in what we publish the article
• Added Interaction Entropy to gmx_MMPBSA output file
• Added a new class to save IE in a csv file
• Added "Go to Top" button to documentation HTML.

Fixes

• Error when ligand and/or receptor are discontinuous (Testing it)
• Error when ligand and/or receptor are discontinuous and numbered non-consecutively
• Non-critical errors and inconsistencies in documentation

Changes

• receptor_mask and ligand_mask have been removed from input file variables. Now we extract the amber mask directly
  based on the GROMACS index file
• The receptor and ligand mapping in the complex was improved. Now we use a method based on the GROMACS index file
• The method Map of the system_MMPBSA class has been restructured. Now always processes amber masks
• Changing the IE calculation function to a class

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