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<div align="center"> <font size="5"> <b><font face="Arial, Helvetica, sans-serif"><a name="top"></a>MCCCS
Towhee (Amber param96)</font></b> </font> </div>
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<td width="697" valign="top"> <b>Overview</b>
<ul>
This section covers the Amber param96 force field as it is implemented into
the Towhee code. All of the Towhee atom types for the Amber param96 force
field are listed, along with a short description of their meanings. For
more information about the Amber force field see the
<a href="http://amber.scripps.edu">Amber web site</a>.
Note that Amber param96 is a Lennard-Jones (12-6) force field and can only be combined with
other Lennard-Jones (12-6) force fields.
I would like to acknowledge Wendy D. Cornell and the late Peter A. Kollman for providing
very useful
guidance about implementing Amber param96. Any discrepencies (especially typos)
from the published Amber param96 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 Amber param96</b>
<ul>
The best literature reference for Amber param96 is
<ul>
<li><a href="../references.html#cornell_et_al_1995">Cornell <i>et al.</i> 1995.</a></li>
</ul>
An electronic version of the Amber param96 parameters can be found at the
<a href="http://amber.scripps.edu">Amber web site</a>.
</ul>
<b>Amber param96 in Towhee</b>
<ul>
The official force field name for Amber param96 in Towhee is 'Amber96' and the file name is
towhee_ff_Amber96 in the ForceFields directory. Here I list all of
the Amber96 atom names for use in the towhee_input file, along with a brief description taken
from the Cornell <i>et al.</i> paper. I have added some comments where I thought clarification
was needed, these are all in [square brackets].
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></dt>
<li><b>'CT'</b> : any sp<sup>3</sup> carbon</li>
<li><b>'C'</b> : any carbonyl sp<sup>2</sup> carbon</li>
<li><b>'CA'</b> : any aromatic sp<sup>2</sup> carbon and (C<sub>epsilon</sub> of Arg)</li>
<li><b>'CM'</b> : any sp<sup>2</sup> carbon, double bonded </li>
<li><b>'CC'</b> : sp<sup>2</sup> aromatic in 5-membered ring with one substituent + next to
nitrogen (C<sub>gamma</sub> in His)</li>
<li><b>'CV'</b> : sp<sup>2</sup> aromatic in 5-membered ring next to carbon and lone pair nitrogen
(e.g. C<sub>delta</sub> in His(delta))</li>
<li><b>'CW'</b> : sp<sup>2</sup> aromatic in 5-membered ring next to carbon and NH (e.g. C<sub>delta</sub> in His(epsilon)
and in Trp)</li>
<li><b>'CR'</b> : sp<sup>2</sup> aromatic in 5-membered ring next to two nitrogens (C<sub>gamma</sub> and C<sub>epsilon</sub>
in His)</li>
<li><b>'CB'</b> : sp<sup>2</sup> aromatic at junction of 5- and 6-membered rings (C<sub>delta</sub> in Trp) and both junction atoms
in Ade and Gua</li>
<li><b>'C*'</b> : sp<sup>2</sup> aromatic in 5-membered ring next to two carbons (e.g. C<sub>gamma</sub> in Trp)</li>
<li><b>'CN'</b> : sp<sup>2</sup> junction between 5- and 6-membered rings and bonded to CH and NH (C<sub>epsilon</sub> in Trp)</li>
<li><b>'CK'</b> : sp<sup>2</sup> carbon in 5-membered aromatic between N and N-R (C8 in purines)</li>
<li><b>'CQ'</b> : sp<sup>2</sup> carbon in 6-membered ring between lone pair nitrogens (e.g. C2 in purines)</li>
<dt><font color="red">Chlorine</font></dt>
<li><b>'Cl-'</b> : ionic chlorine (-1 charge)</li>
<dt><font color="red">Hydrogen</font></dt>
<li><b>'H'</b> : H attached to N</li>
<li><b>'HA'</b> : H attached to aromatic carbon with no electronegative neighbors</li>
<li><b>'HC'</b> : H attached to aliphatic carbon with no electron-withdrawing substituents</li>
<li><b>'H1'</b> : H attached to aliphatic carbon with one electron-withdrawing substituent</li>
<li><b>'H2'</b> : H attached to aliphatic carbon with two electron-withdrawing substituents</li>
<li><b>'H3'</b> : H attached to aliphatic carbon with three electron-withdrawing substituents</li>
<li><b>'HW'</b> : H in TIP3P water</li>
<li><b>'HO'</b> : H in alcohols and acids</li>
<li><b>'HS'</b> : H attached to sulfur</li>
<li><b>'HP'</b> : H attached to carbon directly bonded to formally positive atoms (e.g C next to NH<sub>3</sub><sup>+</sup>
of lysine)</li>
<li><b>'H4'</b> : H attached to aromatic carbon with one electronegative neighbor (e.g hydrogen on C5 of Trp, C6 of Thy)</li>
<li><b>'H5'</b> : H attached to aromatic carbon with two electronegative neighbors (e.g H8 of Ade and Gua and H2 of Ade)</li>
<dt><font color="red">Nitrogen</font></dt>
<li><b>'N'</b> : sp<sup>2</sup> nitrogen in amides</li>
<li><b>'NA'</b> : sp<sup>2</sup> nitrogen in aromatic rings with hydrogen attached (e.g. protonated His, Gua, Trp)</li>
<li><b>'NB'</b> : sp<sup>2</sup> nitrogen in 5-membered ring with lone pair (e.g. N7 in purines)</li>
<li><b>'NC'</b> : sp<sup>2</sup> nitrogen in 6-membered ring with lone pair (e.g. N3 in purines)</li>
<li><b>'N*'</b> : sp<sup>2</sup> nitrogen in 5-membered ring with carbon substituent (in purine nucleosides)</li>
<li><b>'N2'</b> : sp<sup>2</sup> nitrogen of aromatic amines and guanidinium ions</li>
<li><b>'N3'</b> : sp<sup>3</sup> nitrogen</li>
<dt><font color="red">Oxygen</font></dt>
<li><b>'OW'</b> : sp<sup>3</sup> oxygen in TIP3P water</li>
<li><b>'OH'</b> : sp<sup>3</sup> oxygen in alcohols, tyrosine, and protonated carboxylic acids</li>
<li><b>'OS'</b> : sp<sup>3</sup> oxygen in ethers</li>
<li><b>'O'</b> : sp<sup>2</sup> oxygen in amides</li>
<li><b>'O2'</b> : sp<sup>2</sup> oxygen in anionic acids</li>
<dt><font color="red">Phosphorous</font></dt>
<li><b>'P'</b> : phosphorus in phosphates</li>
<dt><font color="red">Sulfur</font></dt>
<li><b>'S'</b> : sulfur in methionine and cysteine [sulfide form of cysteine]</li>
<li><b>'SH'</b> : sulfur in cysteine [thiol form of cysteine]</li>
</ul>
</ul>
<b>Coulombic Interactions</b>
<ul>
Amber 96 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. See the protein section below for comments on the Amber param96 charges used with
the protein builder.
</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. Amber param96 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. 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).
</ul>
<b>Proteins</b>
<ul>
All of the 20 basic amino acids (including the 3 forms of hystidine and the thiol and disulfide forms of cysteine)
are functional for the Amber96 force field. I have implemented the atom types and charges according to the published
Amber param96 values except in the following cases.
<ul>
<li>N-terminal leucine: the electronic files for Amber param96 list CD1 with a charge of -0.41060 and atom CD2 with a charge
of -0.41040. These atoms are symmetric and indistinguishable in reality so I felt it made no sense to give them different
charges just because they have different names. Therefore I put a charge of -0.41050 on both atoms.</li>
<li>N-terminal phenylalanine: the electronic files for Amber param96 list CE1 with a charge of -0.16020 and atom CE2 with a charge
of -0.16030. These atoms are symmetric and indistinguishable in reality so I put a charge of -0.16025 on both atoms.</li>
</ul>
Here is a complete list of the groups for Amber96.
<ul>
<li>'a0' alanine</li>
<li>'c0' cysteine with hydrogen on the sulfur</li>
<li>'cs' cysteine in a disulfide bond</li>
<li>'cp' cysteine bonded to palmitate (includes the palmitate)</li>
<li>'d-' aspartic acid deprotonated</li>
<li>'e-' glutamic acid deprotonated</li>
<li>'f0' phenylalanine</li>
<li>'g0' glycine</li>
<li>'h+' histidine both N protonated</li>
<li>'hd' histidine neutral with only N<sub>d</sub> protonated</li>
<li>'he' histidine neutral with only N<sub>e</sub> protonated</li>
<li>'i0' isoleucine</li>
<li>'k+' lysine protonated</li>
<li>'l0' leucine</li>
<li>'m0' methionine</li>
<li>'n0' asparagine</li>
<li>'p0' proline</li>
<li>'q0' glutamine</li>
<li>'r+' arginine protonated</li>
<li>'s0' serine</li>
<li>'t0' threonine</li>
<li>'v0' valine</li>
<li>'w0' tryptophan</li>
<li>'y0' tyrosine</li>
</ul>
</ul>
<a href="../towhee_capabilities.html">Return to the Towhee Capabilities web 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 -->May 12, 2006<!-- #EndDate -->
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