Upgrading¶

Upgrade to the latest version with:

amber.python -m pip install --upgrade gmx_MMPBSA

Inspect the currently installed version with:

amber.python -m pip show gmx_MMPBSA  or  gmx_MMPBSA -v

Upgrading from 1.4.3 to 1.5.0¶

The new gmx_MMPBSA version 1.5.0 includes major changes in calculation and processing modules, making it incompatible with previous versions.

New variables have been included in the input file to perform new calculations or simply provide the user with full control over the ones already available in gmx_MMPBSA. A number of variables has been also updated, reworked or removed. See the list below for more details:

Variables¶

New variables
- &general namelist
  - c2_entropy
- &gb namelist
  - extdiel
- &pb namelist
  - smoothopt , iprob , arcres , mprob , npbopt , accept , nbuffer , fscale , npbgrid , scalec , nsnba , decompopt , use_rmin , sprob , vprob , rhow_effect , use_sav , maxsph , npbverb
- &rism namelist
  - noasympcorr , ljTolerance , asympKSpaceTolerance , treeDCF , treeTCF , treeCoulomb , treeDCFMAC , treeTCFMAC , treeCoulombMAC , treeDCFOrder , treeTCFOrder , treeCoulombOrder , treeDCFN0 , treeTCFN0 , treeCoulombN0 , mdiis_del , mdiis_nvec , mdiis_restart , maxstep , npropagate , entropicDecomp
Updated variables
- &general namelist
  - PBRadii , interaction_entropy , assign_chainID , solvated_trajectory , verbose
Reworked variables
- &general namelist
  - temperature
Removed variables
- &general namelist
  - protein_forcefield , ligand_forcefield , use_sander

Calculations¶

New calculations
- In the new version, it is possible to perform new calculations such as C2 Entropy and Binding free energy calculation with non-linear PB solver
Updated calculations
- The addition of new variables (see above) provide more control over &pb and &rism calculations

gmx_MMPBSA_ana¶

gmx_MMPBSA_ana has been completely reworked, and it doesn't support files from previous versions. New functions for customizing/exporting graphs, change number of frames and showing/exporting data have been added.

Upgrading from 1.3.x to 1.4.x¶

The differences between both versions are small, you can see them below

Variables¶

New variables in input file
- qh_entropy replace entropy = 1
  
  ( Since v1.4.2)
- interaction_entrpy replace entropy = 2
  
  ( Since v1.4.2)
- ie_segment replace entropy_seg
  
  ( Since v1.4.2)
- forcefields replace protein_forcefield and ligand_forcefield
  
  ( Since v1.4.1)
- temperature replace entropy_temp
  
  ( Since v1.4.1)
- sys_name
  
  ( Since v1.4.0)
- exp_ki
  
  ( Since v1.4.0)
Internal variables (the user only interact with it in the info file)
- complex_fixed (Since v1.4.0)
Modified variables
- print_res (Since v1.4.0)
Deprecated variables
- entropy use qh_entropy or interaction_entropy instead
  
  ( Deprecated: v1.4.2 · Removed: v1.5.0 )
- entropy_seg use ie_segment instead
  
  ( Deprecated: v1.4.2 · Removed: v1.5.0 )
- entropy_temp use temperature instaed
  
  ( Deprecated: v1.4.1 · Removed: v1.5.0 )
- protein_forcefield use forcefields instead
  
  ( Deprecated: v1.4.1 · Removed: v1.5.0 )
- ligand_forcefield use forcefields instead
  
  ( Deprecated: v1.4.1 · Removed: v1.5.0 )

Tip

Check the changes in &general namelist variables section

Command-line¶

gmx_MMPBSA_ana changes the -p option by -f with more flexibility. Please check the gmx_MMPBSA_ana command-line. (Changed in v1.4.0)

Results and info file¶

We have ensured backwards compatibility with gmx_MMPBSA, however there are some changes you can make

Old resultsNew calculation

Since the calculations are done, we only have two options.

Define the variables in gmx_MMPBSA_ana

As we described above, these variables can be defined or modified in the gmx_MMPBSA_ana start dialog (See the gmx_MMPBSA_ana documentation)

Modify the *info file (usually _GMXMMPBSA_info)

Added the new variables as we describe below. We have modified the description in the _GMXMMPBSA_info file a bit to aid editing.

Add variables to _GMXMMPBSA_info file

# You can alter the variables below

INPUT['debug_printlevel'] = 0

INPUT['verbose'] = 2

INPUT['csv_format'] = 1

INPUT['dec_verbose'] = 0

INPUT['temperature'] = 298.15

INPUT['exp_ki'] = 0.0

INPUT['sys_name'] = 'My System'

INPUT['entropy_seg'] = 25

Warning

complex_fixed is an internal variable that cannot be defined in the input file. This variable stores the PDB file name of the fixed complex. This structure corresponds to the complex with the proper chain identifiers and amino acid numbers. If it does not exist, a warning will be displayed, and the complex structure extracted from the structure file defined with the -cs option will be used.

Note that this can lead to inconsistencies, for example: if the file defined in the -cs option is in GRO format, it will not have the string IDs.

You can generate a structure for this variable as follows:

generate a copy of the _GMXMMPBSA_COM.pdb file
Open it with your preferred editor (we recommend one with column editing capabilities, such as Kate, Geany, or Sublime Text)
Check the chains ID, if they do not exist add them
Do not change the numbering of amino acids
Save the document as _GMXMMPBSA_COM_FIXED.pdb

In the _GMXMMPBSA_info file add the following line

FILES.complex_fixed = '_GMXMMPBSA_COM_FIXED.pdb'

save the document

Removing entropy_temp variable

After defining the temperature variable, you can remove the entropy_temp variable. This avoids getting the related warning.

As we describe in the &general namelist variables section in the input file, these three variables are optional since they can be defined or modified in the gmx_MMPBSA_ana start dialog. However, modifying a set of systems can be cumbersome. We recommend defining them in the input file

Example

&general
sys_name="Protein-Ligand",
temperature=310
exp_ki=10
/

Note

exp_ki Only needed when performing correlation analysis

Last update: 2023-06-24
Created: 2023-06-24