4566cd67f9
- Fix an issue where non-existing interactions were analyzed.
Bug fix in setIonDeterminants(): skip interactions if either
titratable_group_interaction_atoms or the backbone_interaction_atoms
is empty.
- Set center of COO_group to self.atom if no oxygens present in residue.
COO_group: If self.atom.get_bonded_elements('O') returns an emtpy list
(the residue has missing side-chain), simply set the center of the
group to the <self.atom> atom, instead of the center of the
(non-existing) oxygens.
- Raise more friendly exception in Group.set_center() if an empty atom
set is passed in.
- Cterm_group: Fix crash if residue is missing a carbon.
The previous code would crash if the C-termini residue group was
missing the carbon atom.
- Fix a failure when a HIS residue has missing side-chain atoms.
- Added an entry for Iodine (I) to the valence electrons table.
PROPKA 3.1
PROPKA predicts the pKa values of ionizable groups in proteins (version 3.0) and protein-ligand complexes (version 3.1) based on the 3D structure.
For proteins without ligands both version should produce the same result.
The method is described in the following papers, which you should cite in publications:
-
Sondergaard, Chresten R., Mats HM Olsson, Michal Rostkowski, and Jan H. Jensen. "Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values." Journal of Chemical Theory and Computation 7, no. 7 (2011): 2284-2295.
-
Olsson, Mats HM, Chresten R. Sondergaard, Michal Rostkowski, and Jan H. Jensen. "PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions." Journal of Chemical Theory and Computation 7, no. 2 (2011): 525-537.
See propka.ki.ku.dk for the PROPKA web server, using the tutorial.
Modifications
This release of PROPKA 3.1 was modified by Oliver Beckstein oliver.beckstein@asu.edu from the released version.
-
Included patches from https://github.com/schrodinger/propka-3.1/tree/python27-compat to make it compatible with Python 2.7
-
Packaged for installation with setuptools.
Installation
Clone repository or unpack the tar ball and install with setuptools (note: if you don't have setuptools installed you will need an internet connection so that the installation procedure can download the required files):
cd propka-3.1
python setup.py install --user
This will install the propka31 script in your executable directory,
as configured for setuptools, for instance ~/.local/bin. You can
change the bin directory with the --install-scripts option. For
example, in order to install in my bin directory in my home
directory:
python setup.py install --user --install-scripts ~/bin
Requirements
- Python 2.7 or higher or Python 3.1 or higher
Getting started
- Clone the code from GitHub
python setup.py install --user- Run
propka31with a .pdb file (see Examples)
Examples
Calculate using pdb file
propka31 1hpx.pdb
Testing (for developers)
Please run Tests/runtest.py/ after changes before pushing commits.
References / Citations
Please cite these references in publications:
-
Sondergaard, Chresten R., Mats HM Olsson, Michal Rostkowski, and Jan H. Jensen. "Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values." Journal of Chemical Theory and Computation 7, no. 7 (2011): 2284-2295.
-
Olsson, Mats HM, Chresten R. Sondergaard, Michal Rostkowski, and Jan H. Jensen. "PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions." Journal of Chemical Theory and Computation 7, no. 2 (2011): 525-537.