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