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PDB2PQR 2.0 which is now available from

PDB2PKA as an alternative to PROPKA for calculating pH values used to protonate residues. This feature is EXPERIMENTAL. The libraries to make this feature available are included in the binary releases. They are NOT included in the source code and are not compiled with the rest of PDB2PQR. Improved web interface. NEW FEATURES

  • Improved look of web interface
  • Option to automatically drop water from pdb file before processing.
  • Integration of PDB2PKA into PDB2PQR as an alternative to PROPKA.
  • Support for compiling with VS2008 in Windows.
  • Option to build with debug headers.
  • PDB2PKA now detects and reports non Henderson-Hasselbalch behavior.
  • PDB2PKA can be instructed whether or not to start from scratch with –pdb2pka-resume
  • Can now specify output directory for PDB2PKA.
  • Improved error regarding backbone in some cases.
  • Changed time format on querystatus page
  • Improved error catching on web interface.

OSX binaries require OSX 10.6 or newer. The OSX binary is 64-bit.

For more information see APBS & PDB2PQR: Electrostatic and solvation properties from complex molecules.

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