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<title>MCCCS Towhee (pdb2towhee)</title>
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<div align="center"> <font size="5"> <b><font face="Arial, Helvetica, sans-serif"><a name="top"></a>MCCCS Towhee (pdb2towhee)</font></b></font></div>
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<dt><b>Overview</b>
<ul>
This section explains the pdb2towhee utility program. This program is designed to translate the standard pdb files into appropriate Towhee files
for starting a simulation. In all cases it will output a <b>towhee_coords</b> file full of the system coordinates. In certain cases it will
output a <b>towhee_altinp</b> file with partial information required to set up a polypeptide molecule template.
</ul>
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<dt><b>Compiling</b>
<ul>
pdb2towhee may be compiled using the Utility Makefile.
<ul>
<dt>cd /towheebase/Utils</dt>
<dt>make pdb2towhee</dt>
</ul>
This will create the pdb2towhee.x executable which can then be run from the command line.
</ul>
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<dt><b>Features</b>
<ul>
When you run this program from the command line it will ask you a number of questions about the file that you wish to translate. Those questions
and a discussion of the available options are listed here.
<dt><b>Please enter the type of input file</b> (integer)
<ul>
<li>1 - protein pdb file
<ul>
This requires the input pdb file to be in the <a href="http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html">standard format</a>,
to have had all of the header information removed (the first line should be the first ATOM line), and to contain a polypeptide that you wish to
input into Towhee using the polypeptide builder. This option will output a <b>towhee_coords</b> file with the system coordinates and a
<b>towhee_altinp</b> file with the listing of amino acids in the Towhee code. You will need to sort through the <b>towhee_altinp</b>
afterwards to sort out the protonation states of histadine, and to assign any bonding partners for disulfide bridges.
</ul>
</li>
<li>2 - generic pdb file
<ul>
This requires the input pdb file to be in the <a href="http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html">standard format</a>,
and to have had all of the header information removed (the first line should be the first ATOM line). This option will output a
<b>towhee_coords</b> file with the system coordinates.
</ul>
</li>
<li>3 - generic Charmm output file
<ul>
This requires the input pdb file to be in the Charmm format and to have had all of the header information removed (the first line should be the
that contains coordinates). This option will output a <b>towhee_coords</b> file with the system coordinates.
</ul>
</li>
<li>4 - Charmm output file (DNA)
<ul>
This requires the input pdb file to be in the Charmm format, to be a DNA strand, and to have had all of the header information removed
(the first line should be the that contains coordinates. This option will output a <b>towhee_coords</b> file with the system coordinates and a
<b>towhee_altinp</b> file with the listing of DNA bases in the Towhee code.
</ul>
</li>
<li>5 - Charmm output file (RNA)
<ul>
This requires the input pdb file to be in the Charmm format, to be a RNA strand, and to have had all of the header information removed
(the first line should be the that contains coordinates. This option outputs a <b>towhee_coords</b> file with the system coordinates and a
<b>towhee_altinp</b> file with the listing of RNA bases in the Towhee code.
</ul>
</li>
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<dt><b>Please enter the pdb file name</b> (character string)
<ul>The name of the file that you wish to translate</ul>
</dt>
<dt><b>Please enter the number of atoms</b> (integer)
<ul>
The number of atoms that you wish to translate from the old file into the Towhee files.
</ul>
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</ul>
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<a href="utility_summary.html">Return to the Utility Summary page</a>
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<i><font size="2">Send comments to:</font></i> <font size="2"> <a href="mailto:marcus_martin@users.sourceforge.net">Marcus G. Martin</a><br>
<i>Last updated:</i> <!-- #BeginDate format:Am1 -->June 11, 2009<!-- #EndDate -->
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