<html>
<head><title>MCCCS Towhee (DREIDING)</title></head>
<body bgcolor="#FFFFFF" text="#000000">
<table width="675" border="0" cellspacing="0" cellpadding="0" height="590">
<tr>
<td colspan="2" height="29">
<div align="center"><font size="5"><b><font face="Arial,Helvetica,sans-serif"><a name="top"></a>MCCCS Towhee (DREIDING)</font></b></font></div>
</td>
</tr>
<A href="http://sourceforge.net">
<IMG src="http://sourceforge.net/sflogo.php?group_id=87039&type=5" width="210" height="62" border="0" alt="SourceForge.net Logo" align="right"/>
</A>
<tr>
<td width="18" height="371" valign="top">
<p> </p>
<p> </p>
</td>
<td width="697" valign="top"> <b>Overview</b>
<ul>
This section covers the DREIDING Force Field as it is implemented into the towhee_ff_DREIDING file in the ForceFields directory. All of the
Towhee atom types for this force field are listed, along with a short description of their meanings. Note that this is a Lennard-Jones force
field and is easilly combined with other similar force fields. You need to use the classical_potential 'Lennard-Jones' for the this force field
and the suggested mixing rules are 'Geometric', although 'Lorentz-Berthelot' is also enabled. Any discrepencies (especially typos) from the
published force field values are the sole responsibility of Marcus G. Martin, and we welcome feedback on how this implementation compares with
other programs.
</ul>
<b>References for DREIDING</b>
<ul>
The parameters implemented here are from Tables I, II, and III of the primary DREIDING paper.
<ul>
<li><a href="../references.html#mayo_et_al_1990">Mayo <i>et al.</i> 1990</a></li>
</ul>
The special hydrogen bonding interactions are not implememted and therefore the atom type 'H___HB' is not included.
</ul>
<b>DREIDING in Towhee</b>
<ul>
The official force field name for DREIDING in Towhee is 'DREIDING'. Here is a list of the atom names for use in the towhee_input file,
along with a brief description taken from the DREIDING literature. DREIDING uses a five-character label to describe every element.
The first two letters are the chemical symbol (appended with an underscore for single letter elements). The third character describes the geometry
of the molecule as follows.
<ul>
<li>1: linear</li>
<li>2: trigonal</li>
<li>R: resonant</li>
<li>3: tetrahedral</li>
</ul>
The fourth and fifth characters are there to help distinguish between otherwise similar atoms (for example, the charge state of metals and
special characters for certain atoms). Towhee follows the DREDING naming convension. Please note that the atom type 'H__HB' is omitted from
this implementation as we did not wish to deal with the special hydrogen bonding interactions that have subsequently fallen out of favor with
most force field developers. The element names are generally obvious (given the rules above), but a notes are added to some potentially confusing
elements, and to the united-atom options. Please note that the capitalization and spacing pattern is important and must be followed exactly
as listed here.
<ul>
<dt><font color="red">All Atom</font></dt>
<li><b>'H_'</b></li>
<li><b>'H_b'</b>: hydrogen bridging between two boron atoms</li>
<li><b>'B_3'</b></li>
<li><b>'B_2'</b></li>
<li><b>'C_3'</b></li>
<li><b>'C_R'</b></li>
<li><b>'C_2'</b></li>
<li><b>'C_1'</b></li>
<li><b>'N_3'</b></li>
<li><b>'N_R'</b></li>
<li><b>'N_2'</b></li>
<li><b>'N_1'</b></li>
<li><b>'O_3'</b></li>
<li><b>'O_R'</b></li>
<li><b>'O_2'</b></li>
<li><b>'O_1'</b></li>
<li><b>'F_'</b></li>
<li><b>'Na_+'</b></li>
<li><b>'Al3'</b></li>
<li><b>'Si3'</b></li>
<li><b>'P_3'</b></li>
<li><b>'S_3'</b></li>
<li><b>'Cl'</b></li>
<li><b>'Ca_+2'</b></li>
<li><b>'Fe_+2'</b></li>
<li><b>'Zn_+2'</b></li>
<li><b>'Ga3'</b></li>
<li><b>'Ge3'</b></li>
<li><b>'As3'</b></li>
<li><b>'Se3'</b></li>
<li><b>'Br'</b></li>
<li><b>'In3'</b></li>
<li><b>'Sn3'</b></li>
<li><b>'Sb3'</b></li>
<li><b>'Te3'</b></li>
<li><b>'I_'</b></li>
<dt><font color="red">United Atom lumping of Hydrogens onto Carbon</font></dt>
<li><b>'C_R1'</b>aromatic carbon plus one bonded hydrogen</li>
<li><b>'C_34'</b>sp<sup>3</sup> carbon plus four bonded hydrogen (methane).</li>
<li><b>'C_33'</b>sp<sup>3</sup> carbon plus three bonded hydrogen (methyl group).</li>
<li><b>'C_32'</b>sp<sup>3</sup> carbon plus two bonded hydrogen (methylene group).</li>
<li><b>'C_31'</b>sp<sup>3</sup> carbon plus one bonded hydrogen (methine group).</li>
</ul>
</ul>
<b>Coulombic interactions</b>
<ul>
The DREIDING paper suggests that the user either ignore charges completely, or assign them using the method of
<a href="../references.html#gasteiger_marsili_1980">Gasteiger and Marsili 1980</a>. Unfortunately, this method is not currently available in Towhee
</ul>
<b>Improper torsions</b>
<ul>
DREIDING uses an improper torsion (called an inversion in their paper) on any atom (I) that is bonded to exactly three other atoms (J,K, and L)
and also has a planar geometry (sp<sup>2</sup> or resonant central atoms). The improper considers the angle each of the vectors (IJ, IK or IL)
makes with a plane described by the other substituants. For example, the angle between the IJ vector and the IKL plane.
Towhee currently requires the user to specify all improper torsions, but you may toggle the type to 0 to allow automatical determination of
the appropriate parameters for each improper torsion.
</ul>
<a href="../towhee_capabilities.html">Return to the Towhee Capabilities web page</a>
<p> </p>
</td>
</tr>
</table>
<hr width="715" align="left">
<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></br>
<i>Last updated:</i><!-- #BeginDate format:Am1 -->December 06, 2006<!-- #EndDate -->
</font>
<br></br>
</body>
</html>
