From owner-chemistry@ccl.net Tue Aug 30 14:12:07 2005 From: "CCL" To: CCL Subject: CCL: W:PDB2PQR Public Release 1.0.0 Message-Id: <-29040-050830101816-14925-sY0f/B+VKit+lcn3g2/sLw]![server.ccl.net> X-Original-From: "Todd J Dolinsky" Sent to CCL by: "Todd J Dolinsky" [todd]![ccb.wustl.edu] Hello Everyone - I am pleased to announce the public release of PDB2PQR 1.0.0, available for download from the new main PDB2PQR page: http://pdb2pqr.sourceforge.net 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 There have been several improvements to the code since its last update, including pKa support via PropKa, a new hydrogen optimization algorithm which should increase both accuracy and speed, and general bug fixes. Two mailing lists have been set up for PDB2PQR discussion - pdb2pqr-announce, for announcements regarding major releases, and pdb2pqr-users for general troubleshooting and help. There are also several trackers on the main sourceforge page for submitting bugs, feature requests, and more. All of these features can be accessed at http://sourceforge.net/projects/pdb2pqr Thanks for your interest! Todd Dolinsky Baker Lab - Washington University in St. Louis todd (at) ccb.wustl.edu From owner-chemistry@ccl.net Tue Aug 30 15:24:45 2005 From: "CCL" To: CCL Subject: CCL: Autodock: Ligand charge error Message-Id: <-29041-050830142159-31726-hrkl3wo+uWKlJqfCv20ZGw]~[server.ccl.net> X-Original-From: Tim Janzen Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 30 Aug 2005 11:42:37 -0400 Mime-Version: 1.0 Sent to CCL by: Tim Janzen [tim.janzen]~[uleth.ca] Hello all, When I read in a ligand with a known charge of 0 into autodock 3.0.5, it returns a charge of -3. This also occurs when I use a -3 form of my ligand, as it returns a -6 charge. Does anyone know why this might be happening? Thanks in advance, Timothy Janzen University of Lethbridge 4401 University Drive, Lethbridge, AB tim.janzen]~[uleth.ca From owner-chemistry@ccl.net Tue Aug 30 22:31:02 2005 From: "CCL" To: CCL Subject: CCL: Help for partial charge of nitrogen atoms in pyrimidine, pyridine and pyrazine Message-Id: <-29042-050830184654-9434-hrkl3wo+uWKlJqfCv20ZGw^_^server.ccl.net> X-Original-From: Minghu Song Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1922002319-1125438407=:43754" Date: Tue, 30 Aug 2005 14:46:47 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Minghu Song [songminghu2004^_^yahoo.com] --0-1922002319-1125438407=:43754 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hello, Dear CCL'rs: I calculated CHELPG partial charge on nitrogen atoms in pyridine, pyrimidine and pyrazine (also 4-azaindole, 4,6-diazaindole and 4,7-diazaindole) for later binding free energy caculation. Based on their pKa and inductive effect, I would expect that the electron density on nitrogen atoms in pyrimidine or 4,6-diazaindole would be smaller than those in pyridine/4-azaindole. (correct me if I am wrong) However, I got larger partial charge on nitrogen atoms in pyrimidine from gaussian calculation: compound CHELPG partial charge on Nitrogen pKa pridine -0.6043 5.1 pyrimidine ~ -0.77 1.3 pyrazine -0.4395 0.6 I used B3LYP/6-31G(d) basis set in the above calculation. I had tried several other basis sets and charges (Mulliken and Merz-Kollman), and obtained the same obseration. Is my assumption wrong? Please share your experience with me. Thanks in advance for you help! Best wishes, Minghu Song Locus Pharmaceuticals --------------------------------- Start your day with Yahoo! - make it your home page --0-1922002319-1125438407=:43754 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hello, Dear CCL'rs:
 
I calculated CHELPG partial charge on nitrogen atoms in pyridine, pyrimidine and pyrazine (also 4-azaindole,  4,6-diazaindole and 4,7-diazaindole) for later binding free energy caculation. 
Based on their pKa and inductive effect,  I would expect that the electron density on nitrogen atoms in pyrimidine or 4,6-diazaindole would be smaller than those in pyridine/4-azaindole.  (correct me if I am wrong) However, I got larger partial charge on nitrogen atoms in pyrimidine from gaussian calculation: 
  
compound                CHELPG partial charge on Nitrogen                    pKa
pridine                                  -0.6043                                                5.1
pyrimidine                           ~  -0.77                                                 1.3
pyrazine                               -0.4395                                                0.6
 
I used B3LYP/6-31G(d) basis set in the above calculation.  I had tried several other basis sets and charges (Mulliken and Merz-Kollman), and obtained the same obseration.  Is my assumption wrong?  Please share your experience with me.  Thanks in advance for you help!
 
Best wishes,
 
Minghu Song
Locus Pharmaceuticals

Start your day with Yahoo! - make it your home page --0-1922002319-1125438407=:43754--