This package contains a regularized Matched Interface and Boundary (rMIB) Poisson-Boltzmann (PB) solver and Python-based wrappers for biological applications. The rMIB PB solver is a smart choice if the accuracy of electrostatic potentials and fields are the major concerns of one's research. Interested users can download the solver (binary) and its wrappers (python source code) and use them for academic purpose by following the New BSD License and citing the related publication as specified below.
This material is based upon work supported by the National Science Foundation under NSF Grant DMS-1318898, DMS-1418957. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.
This software employs a Matched Interface and Boundary (MIB) method with a newly developed two-component decomposition for treating charge sigularities for solving the electrostatic potential under the Poisson-Boltzmann model.
Interested users can download the binary version package (Linux, Mac). Note: For this option, testing proteins in forms of APBS's pqr file (sample) should be stored in the sub-directory with the name of "test_proteins", while MSMS of the corresponding operation system (Linux, Mac), and the input file (sample) should be in the same directory with the binary files. You may also need to change the property of the binary files (rMIB.exe and msms) to executable. More details can be found from the User's Guide.
REFERENCE: W. Geng and S. Zhao, A two-component Matched Interface and Boundary (MIB) regularization for charge singularity in implicit solvation, J. Comput. Phys., 351, 25-39 (2017).
The Python Wrapper pipelines the entire pKa calculation procedure starting from protein data bank file, to calling pdb2pqr (user needs to install pdb2pqr and include it in the system PATH) for generating PQR file, calling rMIB solver for electrostatic energies, and finally return the pKa values for all active sites of the protein. More details can be found from the User's Guide.
Users can download the source code (written in Python by Jingzhen Hu) from pka wrapper.
REFERENCE: J. Hu, S. Zhao, W. Geng, Accurate pKa computation using matched interface and boundary (MIB) method based Poisson-Boltzmann solver, Commun. Comput. Phys., 32(2), 520-539 (2017).