[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

Bug#438092: marked as done (ITP: pdb2pqr -- An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations)

Your message dated Thu, 16 Aug 2007 07:04:40 +0200
with message-id <1187240680.6183.0.camel@localhost>
and subject line dup
has caused the attached Bug report to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what I am
talking about this indicates a serious mail system misconfiguration
somewhere.  Please contact me immediately.)

Debian bug tracking system administrator
(administrator, Debian Bugs database)
--- Begin Message --- 
Package: wnpp
Severity: wishlist
Owner: LI Daobing <lidaobing@gmail.com>

* Package name    : pdb2pqr
  Version         : 1.2.1
  Upstream Author : jens_nielsen, sobolevnrm, todd_dolinsky
* URL             : exec /usr/lib/autossh/autossh
* License         : GPL
  Programming Lang: Python
  Description     : An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann 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.

PDB2PQR uses PROPKA to determine protein pKa values. PROPKA is developed
by the Jensen Research Group at the University of Copenhagen. More
information about PROPKA can be found at http://propka.ki.ku.dk/.

PEOE_PB charges for ligand parameterization were developed by Paul
Czodrowski in the Klebe Group at the Philipps University Marburg.

--- End Message ---
--- Begin Message --- 
See 416269
--- Begin Message --- 
warning: more than one wnpp bug for pdb2pqr, see ITP 438092 and ITP 416269

--- End Message ---

--- End Message ---
Reply to: