justHispKa

justHispKa is an histidine pKa predictor software developed by the Molecular Modeling Team of the Human Health Therapeutics Research Centre, National Research Council Canada.

Click here for download and installation instructions.
Click here to run the program online.

justHispKa has no atom typing capacity and expects proper input molecule preparation. Given the diversity of molecular systems the preparation step is not automated and requires user intervention. The "prep.dir" directory provides some examples of preparation scripts.

justHispKa inputs molecules in Tripos mol2 file formats. Accompanying each input mol2 file, justHispKa requires an Amber parameters (prmtop) file. The user must insure that their molecules are fully parametrized by tleap to produce a prmtop and inpcrd file (refer to the amber manual for instructions).

If relevant cofactors, ions or non-standard aminoacids are present, they must be individually processed with antechamber and loaded in tleap (see the XXXX example). All water molecules and non-structural ions should be removed. It is recommended to add capping groups to truncated chains before running tleap (see the XXXX example).

After successfully running tleap, the ambpdb utility program provided in the ambertools can be used to produce a Tripos mol2 file format that justHispKa can read. Note: the input MOL2 files must contain Tripos atom types (no amber types) in the sixth column of the mol2 ATOM records.

justHispKa MOL=mol2file SID=sid [options]

Where
   MOL=mol2file            Tripos mol2 file containing the protein
   SID=sid                 substructure id of Histidine residue (see note 1)

Available options:
   [PRM=prmtopfile]        amber prmtop parameter file (see note 2)
   [LICENSE=file]          license file location (see note 3)
   [FORCE_HIS=s1,..,sn]    force deprotonated form of listed HIS residue SID(s)
   [FORCE_HIP=s1,..,sn]    force protonated form of listed HIS residue SID(s)
   [FORCE_ASP=s1,..,sn]    force deprotonated form of listed ASP residue SID(s)
   [FORCE_ASH=s1,..,sn]    force protonated form of listed ASP residue SID(s)
   [FORCE_GLU=s1,..,sn]    force deprotonated form of listed GLU residue SID(s)
   [FORCE_GLH=s1,..,sn]    force protonated form of listed GLU residue SID(s)
   [ -b | -brief ]         output only pKa value
   [ -h | -help ]          display program usage and exit
   [ -v | -version ]       display program version and exit

Notes:
   (1) The SID number must correspond to the substructure id given in the mol2 file.
       For example histidine HIS32 on chain B may have SID=134.
   (2) When the PRM filename for a molecule is not given the program will look for a file
       with the same name as the input mol2 files but with suffix ".prmtop".
   (3) The default license file is named "justHispKa.lic" and is expected to be in the sam
       directory as the executable.

In some situation the histidine interacts directly with a titratable residue that could itself alter its protonation. In those situations justHispKa exits with the error message: "multiple titratable groups". It is then possible to force the interacting residu to stay in a specific protonated state with one of the FORCE_xxx arguments.

For example the following commands will give different results:

justHispKa SID=32               # fails with "multiple titratable groups"
justHispKa SID=32 FORCE_ASP=41  # return pka=6.8
justHispKa SID=32 FORCE_ASH=41  # return pka=5.4

By default justHispKa will start 8 POSIX threads for parallel processing. On large multicore computers, the execution time can be reduced by increasing this number with the argument NUM_THREAD=number on the command line. The available memory (RAM) should be ~1Gb per thread.

By default justHispKa reports its results in one line. For example the command:

justHispKa MOL=XXXX.mol2 SID=XX

will return:

DELE=16.738 SESA=31.467 PSESA=22.044 PKA0=4.861 PKA=4.861

The different values are:

  DELE:  the electrostatic score difference between the HIP and HIS forms (Kcal/mole).
  SESA:  the sidechain exposed surface area (Angtrom^2) 
  PSESA: the sidechain exposed polar surface area (Angtrom^2) 
  PKA0:  pKa prediction without the SESA correction (pH units) 
  PKA:   pKa prediction with the SESA correction (pH units) 

If only the pKa value needs to be returned, use the -b option.

If you use justHispKa in your work, please cite:

• Hogues, H., Wei, W. and Sulea, T. (2025). Improved Structure-Based Histidine pKa Prediction for pH-Responsive Protein Design. Journal of Chemical Information and Modeling, 65(3), 1560-1569. [link]

Send feedback, suggestions or queries to mm-admin@nrc-cnrc.gc.ca.