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<h1>PDB2PQR Server</h1>
<P>
<I>Currently using PDB2PQR Version @PDB2PQR_VERSION@</I>
<P>
Return to <a href="http://www.poissonboltzmann.org/docs/structures-ready/"target="BLANK">the PDB2PQR homepage</a>.<br> 	
<hr> 	
This server enables a user to convert <a href="http://www.rcsb.org/pdb/"target="BLANK">PDB</a> files into PQR files.  PQR files are PDB files where the occupancy and B-factor columns have been replaced by per-atom charge and radius.<P>

pKa calculations are performed by <a href="https://github.com/jensengroup/propka-3.1"target="BLANK">PROPKA</a>.<P>

For more information on PDB2PQR please see the:<br />
<ul>
	<li> <a href="http://www.poissonboltzmann.org/docs/structures-ready/"target="BLANK">Home Page</a> </li>
	<li> <a href="http://eepurl.com/by4eQr"target="BLANK">Register (and help suport PDB2PQR & APBS)</a> </li>
	<li> <a href="http://www.poissonboltzmann.org/docs/pdb2pqr-programmers/"target="BLANK">User Guide</a> </li>
	<li> <a href="http://www.poissonboltzmann.org/examples/home/"target="BLANK">Examples</a> </li>
	<li> <a href="https://github.com/Electrostatics/apbs-pdb2pqr/releases/tag/pdb2pqr-2.1.0_release"target="BLANK">Release Notes</a> </li>
</ul>

If you use the PDB2PQR service in a publication, please cite:
<blockquote>Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. <I>Nucleic Acids Research</I> <B>32</B> W665-W667 (2004). [<a href="http://nar.oupjournals.org/cgi/content/abstract/32/suppl_2/W665" target="BLANK">Link</a>]
</blockquote>

<hr>
@WITHOPAL@
<B>Note:</B> In order to distribute server load, the PDB2PQR server currently
is limited to a maximum size of @MAXATOMS@ atoms per protein.  If you are interested
in using PDB2PQR for larger proteins, you are encouraged to download a command
line version of PDB2PQR from the <a
	href="http://www.poissonboltzmann.org/docs/downloads/"target="BLANK">PDB2PQR download page</a>.  For
additional limitations, please see the <a
	href="http://www.poissonboltzmann.org/docs/pdb2pqr-programmers/"target="BLANK">PDB2PQR user
	guide</a> <P>
<B>Note:</B> This server uses automatic refreshing to update the status of your PDB2PQR submission.  Do not use the <i>back</i> button on your browser while the server is running.<P>
@WITHOPAL@
@WITHOUTOPAL@
<B>Note:</B> This server uses automatic refreshing to update the status of your PDB2PQR submission.<P>
@WITHOUTOPAL@

<FORM action="@action@" METHOD="POST" ENCTYPE="multipart/form-data" name="thisform">

Please enter either:
<blockquote>
<input type="RADIO" name="PDBSOURCE" value="ID" onClick="check(this.value)" CHECKED>a PDB ID</input>: <input type="text" name="PDBID" size=4 maxlength=6 value=""> <br />
<input type="RADIO" name="PDBSOURCE" value="UPLOAD" onClick="check(this.value)">upload a PDB file</input>: <input type="file" name="PDB" size="25" maxlength=100 value="" DISABLED>
</blockquote>
<P>

Pick a forcefield to use: 
<blockquote>
<input type="RADIO" name="FF" id = "amber" value="amber" onClick="setff(this.value)">AMBER</input><br /> 
<input type="RADIO" name="FF" id = "charmm" value="charmm" onClick="setff(this.value)">CHARMM</input><br />
<input type="RADIO" name="FF" id = "parse" value="parse" onClick="setff(this.value)" CHECKED >PARSE</input><br />
<input type="RADIO" name="FF" id = "peoepb" value="peoepb" onClick="setff(this.value)">PEOEPB</input><br />
<input type="RADIO" name="FF" id = "swanson" value="swanson" onClick="setff(this.value)">SWANSON</input><br /> 
<input type="RADIO" name="FF" id = "tyl06" value="tyl06" onClick="setff(this.value)">TYL06</input><br />
<input type="RADIO" name="FF" id = "user" value="user" onClick="setff(this.value)">User-defined forcefield (<a href="http://www.poissonboltzmann.org/docs/pdb2pqr-faq/"target="BLANK">help</a>): <input type="file" name="USERFF" size="25" maxlength=100 value="" DISABLED><br />
<label>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;User-defined names (<a href="http://www.poissonboltzmann.org/docs/pdb2pqr-faq/"target="BLANK">help</a>):</label> <input type="file" name="USERNAMES" size="25" maxlength=100 value="" DISABLED><br />
<label>&nbsp;&nbsp;* If you select user-defined forcefield, you also need to specify a user-defined .names file.</label><br /> 
</blockquote>

Pick an output naming scheme to use (<a href="http://www.poissonboltzmann.org/docs/pdb2pqr-faq/"target="BLANK">help</a>):
<blockquote>
<input type="RADIO" name="FFOUT" value="internal" CHECKED>Internal naming scheme</input> (<a href="http://www.poissonboltzmann.org/docs/pdb2pqr-programmers/"target="BLANK">What's this?</a>)<br />
<input type="RADIO" name="FFOUT" value="amber">AMBER</input><br />
<input type="RADIO" name="FFOUT" value="charmm">CHARMM</input><br />
<input type="RADIO" name="FFOUT" value="parse">PARSE</input><br />
<input type="RADIO" name="FFOUT" value="peoepb">PEOEPB</input><br />
<input type="RADIO" name="FFOUT" value="swanson">SWANSON</input><br />
<input type="RADIO" name="FFOUT" value="tyl06">TYL06</input>

</blockquote>

Available options: 
<blockquote>
<input type="CHECKBOX" name="DEBUMP" CHECKED> Ensure that new atoms are not rebuilt too close to existing atoms<br />
<input type="CHECKBOX" name="OPT" CHECKED onClick="setwatopt()"> Optimize the hydrogen bonding network<br />
<input type="CHECKBOX" name="LIGANDCHECK" onClick="setligand()"> Assign charges to the ligand specified in a MOL2 file</input>: <input type="file" name="LIGAND" size="25" maxlength=100 value="" DISABLED><br />
<input type="CHECKBOX" name="INPUT" CHECKED> Create an <a href="http://www.poissonboltzmann.org/docs/calculating/"target="BLANK">APBS</a> input file <span style="font-size:60%">(this also enables the option to run APBS and visualize your results through the web interface, if it has been installed)</span><br />
<input type="CHECKBOX" name="CHAIN"> Add/keep chain IDs in the PQR file<br />
<input type="CHECKBOX" name="WHITESPACE"> Insert whitespaces between atom name and residue name, between x and y, and between y and z<br />
<input type="CHECKBOX" name="TYPEMAP"> Create Typemap output<br />
<input type="CHECKBOX" name="NEUTRALN" onClick="setneutraln()"> Make the protein's N-terminus neutral (requires PARSE forcefield)<br />
<input type="CHECKBOX" name="NEUTRALC" onClick="setneutralc()"> Make the protein's C-terminus neutral (requires PARSE forcefield)<br />
<input type="CHECKBOX" name="DROPWATER"> Remove the waters from the output file
</blockquote>

pKa Options*:
<blockquote>
Use pH <input type="text" name="PH" size=4 maxlength=6  value="7"></input><br />
<input type="RADIO" name="PKACALCMETHOD" value="none" id="pka_none" onClick="setpkamethod(this.value)"> No pKa calculation</input><br />
<input type="RADIO" name="PKACALCMETHOD" value="propka" id="pka_propka" onClick="setpkamethod(this.value)" CHECKED> Use <a href="https://github.com/jensengroup/propka-3.1"target="BLANK">PROPKA</a> to assign protonation states at provided pH</input><br />
<input type="RADIO" name="PKACALCMETHOD" value="pdb2pka" id="pka_pdb2pka" onClick="setpkamethod(this.value)"> Use PDB2PKA to parametrize ligands and assign pKa values (requires PARSE forcefield) at provided pH</input><br />

@WITHOUTOPAL@
<label>&nbsp;&nbsp;* Warning: PDB2PKA is currently experimental and the process can take a very long time.</label>
@WITHOUTOPAL@
@WITHOPAL@
<label>&nbsp;&nbsp;* Warning: PDB2PKA is currently experimental and the process can take a very long time. The webserver will kill any jobs that last longer than one week. </label>
@WITHOPAL@
See the 
<a
href="https://github.com/Electrostatics/apbs-pdb2pqr/releases/tag/pdb2pqr-2.1.0_release"target="BLANK">Release
Notes</a> for changes since the last version.

</blockquote>

<input type="submit" value="Submit"><P>
</form> 
<HR>
The PDB2PQR application and web server was written by:
<blockquote>
Jens Erik Nielsen<br />
Todd Dolinsky<br />
<a href="http://www.linkedin.com/in/nathanandrewbaker"target="BLANK">Nathan Baker</a><br />
Kyle Monson<P>
</blockquote>
PDB2PQR <a href="http://nbcr-222.ucsd.edu/opal2/dashboard"target="BLANK">Opal </a>integration by: <br />
<blockquote>
Wes Goodman<br />
Samir Unni<br />
Yong Huang<P>
</blockquote>
3dMol visualization provided by:
<blockquote>
<a href="http://3dmol.csb.pitt.edu/"target="BLANK">David Koes</a><P>
</blockquote>
JMol visualization scripts and applets provided by:
<blockquote>
<a href="http://chemapps.stolaf.edu/jmol"target="BLANK">Robert Hanson</a><P>
</blockquote>

PDB2PQR is supported by NIH grant GM069702-01 to NAB, the NPACI Alpha Project program, and the <a href="http://www.btrportal.org/centers/national-biomedical-computation-resource"target="BLANK"> National Biomedical Computation Resource</a>.<P>
Before sending a bug report you may want to check the <a href="http://sourceforge.net/p/pdb2pqr/mailman/pdb2pqr-users/"target="BLANK">pdb2pqr-users mailing list archives</a> to make sure your question has not already been addressed.<P>
For additional support, feature requests, and bug reports you may contact the <a href="https://lists.sourceforge.net/lists/listinfo/pdb2pqr-users"target="BLANK">pdb2pqr-users mailing list</a>.<P>
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