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  • Last update: 5 years ago
  • Total downloads: 78
  • Operating system: Win All
  • Publisher: poissonboltzmann.org
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windows default iconPDB2PQR Publisher's description

PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations

PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include:

Adding a limited number of missing heavy atoms to biomolecular structures
Determining side-chain pKas
Placing missing hydrogens
Optimizing the protein for favorable hydrogen bonding
Assigning charge and radius parameters from a variety of force fields

PDB2PQR was ported to Python by Todd Dolinsky while working with Nathan Baker at Washington University in St. Louis. The PDB2PQR code is based on C++ design and algorithms by Jens Erik Nielsen. PDB2PQR was originally designed to facilitate structure preparation for APBS.

What's New in This Release:

New Features:
В· Switched Opal service urls from sccne.wustl.edu to NBCR.
В· Added more JMol controls for visualization, JMol code and applets provided by Bob Hanson.
В· Changed default forcefield to PARSE in web interface.
В· Improved interface to extensions. Extensions may now add their own command line options.

Bug Fixes:
В· Fixed crash when opal returns an error.
В· Fixed specific combinations of commandline arguments causing pdb2pqr.py to crash.
В· Fixed opal job failing when filenames have spaces or dashs.
В· Fixed gap in backbone causing irrationally placed hydrogens.
В· Fixed crash when too many fixes are needed when setting termini.
В· Corrected web and command line error handling in many cases.
В· Fixed --username command line option.
В· Fixed ambiguous user created forcefield and name handling. Now --username is required if --userff is used.
В· Fixed querystatus.py not redirecting to generated error page.

System Requirements:

В· Python
Program Release Status: New Release
Program Install Support: Install and Uninstall

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