Macs in Chemistry

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PDB2PQR 2.1 released

 

A new version of PDB2PQR has been released.

APBS (Adaptive Poisson-Boltzmann Solver) and PDB2PQR are software packages designed to help you analyze the solvation properties of small and macro-molecules such as proteins, nucleic acids, and other complex systems

  • Added alternate method to do visualization using 3dmol.
  • Replaced the Monte Carlo method for generating titration curves with graph cut. See http://arxiv.org/abs/1507.07021 (If you prefer the Monte Carlo method, please use http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/)
  • Added compile options to allow for arbitrary flags to be added. Helps work around some platforms where scons does not detect the needed settings correctly.
  • Added a check before calculating pKa's for large interactions energies.

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

Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res, 35, W522-5, 2007. DOI

Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res, 32, W665-W667, 2004. DOI


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