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<div align="center"> <font size="5"> <b><font face="Arial, Helvetica, sans-serif"><a name="top"></a>MCCCS
Towhee (Weiner et al 1984)</font></b> </font> </div>
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<td width="697" valign="top"> <b>Overview</b>
<ul>
This section covers an early force field in the Amber family called the Weiner <i>et al.</i> 1984 force field
as it is implemented into the Towhee code. All of the Towhee atom types for the Weiner <i>et al.</i> 1984 force
field are listed, along with a short description of their meanings. For
more information about the Amber family of force fields see the <a href="http://amber.scripps.edu">Amber web site</a>.
Weiner <i>et al.</i> 1984 is a united-atom force field that was later expanded, and slightly modified,
to allow some all atom types along side of the united atom types. See <a href="weiner1986.html">Weiner <i>et al.</i> 1986</a>
for more information about this extension.
Note that Weiner <i>et al.</i> 1984 is a 12-6 plus 12-10 H-bond force field and can only be combined with
other '12-6 plus 12-10 H-bond' force fields.
Any discrepencies (especially typos) from the published force field values are the sole responsibility
of Marcus G. Martin, and I welcome feedback on how this implementation compares with other programs.
<p> </p>
</ul>
<b>References for Weiner <i>et al.</i> 1984</b>
<ul>
<ul>
<li><a href="../references.html#weiner_et_al_1984">Weiner <i>et al.</i> 1984.</a></li>
</ul>
</ul>
<b>Weiner <i>et al.</i> 1984 in Towhee</b>
<ul>
The official force field name for Weiner <i>et al.</i> in Towhee is 'Weiner1984' and the file name is
towhee_ff_Weiner1984 in the ForceFields directory. Here I list all of
the atom names for use in the towhee_input file, along with a brief description taken
from the <a href="../references.html#weiner_et_al_1984">Weiner <i>et al.</i> 1984</a> paper.
Please note that the capitalization and spacing pattern is important
and must be followed exactly as listed here.
<ul>
<dt><font color="red">Carbon</font> (united or atomic)</dt>
<li><b>'C2'</b> : united sp<sup>3</sup> carbon with two hydrogens</li>
<li><b>'C3'</b> : united sp<sup>3</sup> carbon with three hydrogens</li>
<li><b>'CD'</b> : united sp<sup>2</sup> aromatic carbon in six-membered ring with one hydrogen</li>
<li><b>'CE'</b> : united sp<sup>2</sup> aromatic carbon in five-membered ring between two nitrogens with
one hydrogen (in purines)</li>
<li><b>'CF'</b> : united sp<sup>2</sup> aromatic carbon in five-membered ring next to a nitrogen without a
hydrogen (e.g., C<sub>delta</sub>-N<sub>epsilon</sub>=C<sub>epsilon</sub> in histidine)</li>
<li><b>'CG'</b> : united sp<sup>2</sup> aromatic carbon in five membered ring next to a N-H
(e.g., C<sub>delta</sub>-N<sub>epsilon</sub>=C<sub>epsilon</sub> in histidine)</li>
<li><b>'CH'</b> : united sp<sup>3</sup> carbon with one hydrogen</li>
<li><b>'CI'</b> : united sp<sup>2</sup> carbon in six-membered ring of purines between two "NC" nitrogens</li>
<li><b>'CJ'</b> : united sp<sup>2</sup> carbon in pyrimidines at positions 5 and 6 (more pure double bond
than aromatic) with one hydrogen</li>
<li><b>'CP'</b> : united sp<sup>2</sup> aromatic carbon in five-membered ring between two nitrogens with one hydrogen (in His)</li>
<li><b>'C'</b> : atomic sp<sup>2</sup> carbonyl carbon and aromatic carbon with hydroxyl substituent in tyrosine</li>
<li><b>'C*'</b> : atomic sp<sup>2</sup> aromatic carbon in five-membered ring with one substituent
(e.g., CE<sub>gamma</sub> in Trp)</li>
<li><b>'CA'</b> : atomic sp<sup>2</sup> aromatic carbon in six-membered ring with one substituent</li>
<li><b>'CB'</b> : atomic sp<sup>2</sup> aromatic carbon at junction between five- and six-membered rings (e.g., CE<sub>delta</sub>
in Trp, C4 and C5 in purines)</li>
<li><b>'CC'</b> : atomic sp<sup>2</sup> aromatic carbon in five-membered ring with one substituent and next to a nitrogen group
(e.g., C<sub>gamma</sub> in His)</li>
<li><b>'CM'</b> : atomic sp<sup>2</sup> same as CJ but one substituent</li>
<li><b>'CN'</b> : atomic sp<sup>2</sup> aromatic junction carbon in between five- and six-membered rings (e.g., C<sub>epsilon</sub>
in Trp)</li>
<li><b>'CT'</b> : atomic sp<sup>3</sup> carbon with four explicit substituents</li>
<dt><font color="red">Hydrogen</font> (all atomic)</dt>
<li><b>'H3'</b> : hydrogens of lysine and arginine (positively charged)</li>
<li><b>'H2'</b> : amino hydrogens from NH<sub>2</sub> in purines and pyrimidines</li>
<li><b>'HC'</b> : explicit hydrogen attached to carbon</li>
<li><b>'H'</b> : amide and imino hydrogens</li>
<li><b>'HO'</b> : hydrogen on hydroxyl or water oxygen</li>
<li><b>'HS'</b> : hydrogen attached to sulfur</li>
<dt><font color="red">Nitrogen</font> (all atomic)</dt>
<li><b>'NC'</b> : sp<sup>2</sup> nitrogen in six-membered ring with lone pairs (e.g., N3 in adenine)</li>
<li><b>'NA'</b> : sp<sup>2</sup> nitrogen in five-membered ring with hydrogen attached (e.g., protonated His)</li>
<li><b>'NB'</b> : sp<sup>2</sup> nitrogen in five-membered ring with lone pairs (e.g., N7 in purines)</li>
<li><b>'N*'</b> : sp<sup>2</sup> nitrogen in purines and pyrimidines with alkyl group attached
(N9 in purines. N1 in pyrimidines)</li>
<li><b>'N'</b> : sp<sup>2</sup> nitrogen in amide groups</li>
<li><b>'N2'</b> : sp<sup>2</sup> nitrogen in base NH<sub>2</sub> groups and arginines NH<sub>2</sub></li>
<li><b>'N3'</b> : sp<sup>3</sup> nitrogen with four substituents (e.g., Lys N<sub>zeta</sub></li>
<li><b>'NT'</b> : sp<sup>3</sup> nitrogen with three substituents (e.g., unprotonated amines)</li>
<dt><font color="red">Oxygen</font> (all atomic)</dt>
<li><b>'O'</b> : carbonyl oxygen</li>
<li><b>'O2'</b> : corboxyl and phosphate nonbonded oxygens</li>
<li><b>'OS'</b> : ether and ester oxygens</li>
<li><b>'OH'</b> : alcohol oxygens</li>
<dt><font color="red">Phosphorus</font> (all atomic)</dt>
<li><b>'P'</b> : phosphorus in phosphate groups</li>
<dt><font color="red">Sulfur</font> (all atomic)</dt>
<li><b>'S'</b> : sulfurs in disulfide linkages and mentioning</li>
<li><b>'SH'</b> : sulfur in cycstine</li>
<li><b>'LP'</b> : lone pairs attached to sulfur</li>
</ul>
</ul>
<b>Coulombic Interactions</b>
<ul>
Weiner <i>et al.</i> 1984 uses point charges located at atomic centers to represent the elecrostatic interactions between atoms.
There is no simple, general table of charges for atoms in this force field. Instead, they recommend using the RESP
method to fit the charges for each molecule of interest.
See the <a href="http://amber.scripps.edu">Amber web site</a>
for more information about this method.
</ul>
<b>Improper torsions</b>
<ul>
Improper torsions are not automatically generated by the Towhee code as the rules for determining where they are applied
are not always straight-forward. Weiner <i>et al.</i> exclusively uses the Stereocenter version of the improper torsions, and they
are typically centered on an sp<sup>2</sup> atom in order to enforce planarity with its three neighbors. However, they are
also centered on some united-atoms in order to enforce stereochemistry. Only one
improper torsion allowed to be centered on any atom. These torsions are listed in the Amber literature as i-j-k-l where the
angle is the dihedral between i-k-l and j-k-l, and the bonding pattern is i, j, and l are all bonded to atom k, and are also not
bonded to each other. In the towhee_input file this stereo improper torsion is listed only for atom k, and the atom order there
is l, i, j. Remember that you can set the improper type to 0 to have the code automatically determine the improper type (so long
as inpstyle is 2). Please see the <a href="../references.html#weiner_et_al_1984">Weiner <i>et al.</i> 1984</a> paper for more
information about assigning improper torsions for this force field.
</ul>
<b>Proteins</b>
<ul>
This force field contains parameters for all of the amino acids, but these have not yet been implemented into the
polymer builder in Towhee. If anyone is interested in implementing this functionality for this force field please
contact the Towhee developers.
</ul>
<a href="../towhee_capabilities.html">Return to the Towhee Capabilities web page</a>
<p> </p>
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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 -->September 07, 2005<!-- #EndDate -->
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