Most users will likely interact with PDB2PQR through the servers listed at Web servers. However, it is also possible to install local versions of PDB2PQR. These local installations not only provide a web server but also give a command line version of the PDB2PQR software that can be customized through a variety of extensions.
The PDB2PQR source code can be downloaded. As the bulk of the PDB2PQR code is written Python, the PDB2PQR code itself is architecture- and compiler-independent. PDB2PQR has been tested using Python versions 2.6-2.7 and Numeric version 24.2 - problems may occur with other versions. Users who simply want to use the PDB2PQR without PROPKA or ligand parameterization support can unarchive the source code, change to the top-level source code directory, and type
$ ./configure --disable-propka --disable-pdb2pka
or skip the configure/make process altogether.
To use PROPKA with PDB2PQR, a three step installation is necessary, making use of available C and Fortran compilers:
This should compile the PROPKA wrappers necessary to interface with PDB2PQR. If the compilation fails, please send a bug report.
PDB2PKA is the PDB2PQR library that includes both ligand parameterization and Poisson-Boltzmann-based pKa calculation routines. This code is written in C++ and Python. This portion of the code also requires the Python Numeric or NumPy package. Note that PDB2PQR has only been extensively tested against Numeric. Unlike earlier versions, PDB2PKA is enabled by default in this version. To use PDB2PKA with PDB2PQR, a three step installation is necessary, making use of available C and Fortran compilers:
This should compile the PDB2PKA wrappers necessary to interface with PDB2PQR. Note that this will also compile PROPKA supprot; this can be explicitly disabled by
$ ./configure --enable-pdb2pka --disable-propka
If the compilation fails, please send a bug report.
All the necessary files for web server installation are available with the PDB2PQR software; however, we would appreciate if users contact us before installing a publicly-accessible version of the web server so we can ensure that you are informed of PBD2PQR updates, etc.
Note: these instructions are intended for systems administrators with the ability to change the behavior of their web server software and/or install software in privileged locations. To set up a server, simply run
By default, the server is installed in
Configure options include
It is highly recommended that
If the server interface loads fine, but you cannot execute pdb2pqr by clicking the "Submit" button, make sure you have the permission to execute