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<title>MCCCS Towhee (OPLS-ua)</title>
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<div align="center"> <font size="5"> <b><font face="Arial, Helvetica, sans-serif"><a name="top"></a>MCCCS
Towhee (OPLS-ua)</font></b> </font> </div>
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<td width="697" valign="top"> <b>Overview</b>
<ul>
This section covers the OPLS-ua force field as it is implemented into the towhee_ff_OPLS-ua file in the
ForceFields directory. All of the Towhee atom types for the OPLS-ua force field
are listed, along with a short description of their meanings. For more
information about the OPLS family of force fields see the <a href="http://zarbi.chem.yale.edu/">Jorgensen
group home page</a>. Note that OPLS-ua is a Lennard-Jones (12-6) force
field and can only be combined with other Lennard-Jones (12-6) force fields.
The rather famous OPLS water models are not included here as they are provided in their own
force field files. Please see the <a href="tip3p.html">TIP3P</a>, <a href="tip4p.html">TIP4P</a>,
and <a href="tip5p.html">TIP5P</a> web pages for more information about those water models.
Note that OPLS-ua was followed up with an all-atom version of the force field
called <a href="oplsaa.html">OPLS-aa</a>
and has been reparameterized into what I call <a href="opls2001.html">OPLS-2001</a>.
Any discrepencies (especially typos) from the published OPLS-ua 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 OPLS-ua</b>
<ul>
OPLS-ua is published in a series of papers
<ul>
<li><a href="../references.html#chandrasekhar_et_al_1984">Chandrasekhar <i>et al.</i> 1984</a></li>
<li><a href="../references.html#cournoyer_jorgensen_1984">Cournoyer and Jorgensen 1984</a></li>
<li><a href="../references.html#jorgensen_et_al_1984">Jorgensen <i>et al.</i> 1984</a></li>
<li><a href="../references.html#jorgensen_swenson_1985">Jorgensen and Swenson 1985</a></li>
<li><a href="../references.html#jorgensen_1986_alcohol">Jorgensen 1986 alcohol</a></li>
<li><a href="../references.html#jorgensen_1986_sulfur">Jorgensen 1986 sulfur</a></li>
<li><a href="../references.html#jorgensen_briggs_1988">Jorgensen and Briggs 1988</a></li>
<li><a href="../references.html#jorgensen_et_al_1990">Jorgensen <i>et al.</i> 1990</a></li>
</ul>
</ul>
<b>OPLS-ua in Towhee</b>
<ul>
The official force field name for OPLS-ua in Towhee is 'OPLS-ua'. Here
I list all of the OPLS-ua atom names for use in the towhee_input file,
along with a brief description taken from the OPLS-ua literature. I
have used my own judgement in creating naming conventions as they
are not well defined in the literature. Please note that the capitalization and
spacing pattern is important and must be followed exactly as listed here.
<ul>
<dt><font color="red">Carbon (CH<sub>3</sub> United-Atoms)</font></dt>
<li><b>'CH4'</b> : United-atom Methane</li>
<li><b>'CH3-C1'</b> : CH<sub>3</sub> united-atom consisting of 1 C
and 3 H that is bonded to another carbon that is not in turn bonded
to any other carbons(example: ethane methyl group, acetonitrile methyl group)</li>
<li><b>'CH3-C2'</b> : CH<sub>3</sub> united-atom consisting of 1 C
and 3 H that is bonded to another carbon that has 2 non-H
neighbors (example: n-alkane methyl group), or is bonded to a sulfur that
is in turn bonded to a hydrogen (example: thiols).</li>
<li><b>'CH3-C3'</b> : CH<sub>3</sub> united-atom consisting of 1 C
and 3 H that is bonded to another carbon that has 3 non-H neighbors
(example: isobutane methyl group).</li>
<li><b>'CH3-C4'</b> : CH<sub>3</sub> united-atom consisting of 1 C
and 3 H that is bonded to another carbon that has 4 non-H neighbors
(example: neopentane methyl group)</li>
<li><b>'CH3-X'</b> : CH<sub>3</sub> united-atom consisting of 1 C
and 3 H that is bonded to an atom other than carbon that is in turn bonded to another
non-hydrogen atom or more than one hydrogram atom
(example: sulfides, disulfides, N-methylacetamide, dimethylformamide, methyl-acetate).</li>
<dt><font color="red">Carbon (CH<sub>2</sub> United-Atoms)</font></dt>
<li><b>'CH2sp3-SR'</b> : CH<sub>2</sub> united-atom consisting of 1 C
and 2 H with an <i>sp<sup>3</sup></i> hybridization on the C that is bonded
to a sulfur that is in turn bonded to another non-hydrogen atom
(example: sulfides and disulfides).</li>
<li><b>'CH2sp3-N'</b> : CH<sub>2</sub> united-atom consisting of 1 C
and 2 H with an <i>sp<sup>3</sup></i> hybridization on the C that is bonded
to a nitrogen (example: C<sub>alpha</sub> in glycine, C in proline).</li>
<li><b>'CH2sp3'</b> : CH<sub>2</sub> united-atom consisting of 1 C
and 2 H with an <i>sp<sup>3</sup></i> hybridization on the C.</li>
<li><b>'CH2sp2'</b> : CH<sub>2</sub> united-atom consisting of 1 C
and 2 H with an <i>sp<sup>2</sup></i> hybridization on the C.</li>
<dt><font color="red">Carbon (CH United-Atoms)</font></dt>
<li><b>'CHsp3-N'</b> : CH united-atom consisting of 1 C
and 1 H with an <i>sp<sup>3</sup></i> hybridization on the C that is
bonded to a Nitrogen (example: C<sub>alpha</sub> in Ala, C<sub>alpha</sub> in Pro).</li>
<li><b>'CHsp3'</b> : CH united-atom consisting of 1 C
and 1 H with an <i>sp<sup>3</sup></i> hybridization on the C.</li>
<li><b>'CHsp2-N'</b> : CH united-atom consisting of 1 C
and 1 H with an <i>sp<sup>2</sup></i> hybridization on the C that is
bonded to a Nitrogen (example: formamide).</li>
<li><b>'CHsp2'</b> : CH united-atom consisting of 1 C
and 1 H with an <i>sp<sup>2</sup></i> hybridization on the C.</li>
<li><b>'CHarom'</b> : CH united-atom consisting of 1 C
and 1 H with an aromatic C.</li>
<dt><font color="red">Carbon Atoms</font></dt>
<li><b>'Csp3'</b> : C atom consisting of 1 C bonded to 0 H
with an <i>sp<sup>3</sup></i> hybridization on the C.</li>
<li><b>'Csp2'</b> : C atom consisting of 1 C bonded to 0 H
with an <i>sp<sup>2</sup></i> hybridization on the C.</li>
<li><b>'Csp'</b> : C atom consisting of 1 C bonded to 0 H
with an <i>sp</i> hybridization on the C (example: central C in acetonitrile).</li>
<dt><font color="red">Chlorine</font></dt>
<li><b>'Cl-'</b> : Cl ion with a negative 1.0 charge.</li>
<dt><font color="red">Fluorine</font></dt>
<li><b>'F'</b> : F in Hydrogen Fluoride.</li>
<li><b>'F-'</b> : F ion with a negative 1.0 charge.</li>
<dt><font color="red">Hydrogen</font></dt>
<li><b>'H'</b> : H atom bonded to something other than a carbon.</li>
<dt><font color="red">Lithium</font></dt>
<li><b>'Li+'</b> : Li ion with a positive 1.0 charge.</li>
<dt><font color="red">Nitrogen</font></dt>
<li><b>'Nsp2'</b> : Nitrogen bonded to 3 other atoms in a trigonal planar arrangement
(example: amides and amino acids).</li>
<li><b>'Ns'</b> : Nitrogen triple bonded to one other atom (example: acetonitrile).</li>
<dt><font color="red">Oxygen</font></dt>
<li><b>'Osp3'</b> : sp<sup>3</sup> hybridization on an O atom that is bonded
to two other atoms.</li>
<dt><font color="red">Sodium</font></dt>
<li><b>'Na+'</b> : Na ion with a positive 1.0 charge.</li>
<dt><font color="red">Sulfur</font></dt>
<li><b>'S-HSH'</b> : sulfur bonded to 2 hydrogen atoms.</li>
<li><b>'S-RSR'</b> : sulfur bonded to 2 atoms where at least one of those atoms
is not a hydrogen.</li>
</ul>
</ul>
<b>Coulombic interactions</b>
<ul>
OPLS-ua uses atom-centered point charges to represent the electrostatic interactions.
You need to look through the <a href="../references.html#force_fields_opls">OPLS-ua literature</a> to find
molecules with similar moieties to the ones on the molecule you wish to simulate. Here I list some examples.
<dt>Alcohols (from <a href="../references.html#jorgensen_1986_alcohol">Jorgensen 1986 alcohols</a>)
<ul>
<li><b>'H'</b>: -0.700</li>
<li><b>'Osp3'</b>: 0.435</li>
<li><b>'C'</b> that is bonded directly to the oxygen: 0.265</li>
</ul>
</dt>
<dt>Thiols (from <a href="../references.html#jorgensen_1986_sulfur">Jorgensen 1986 sulfur</a>)
<ul>
<li><b>'H'</b>: 0.27</li>
<li><b>'S-RSR'</b>: -0.45</li>
<li><b>'CH*'</b> bonded to the thiol sulfur: 0.18</li>
</ul>
</dt>
<dt>Sulfides (from <a href="../references.html#jorgensen_1986_sulfur">Jorgensen 1986 sulfur</a>)
<ul>
<li><b>'CH3-SR'</b> or <b>'CH2sp3-SR'</b>: 0.235</li>
<li><b>'S-RSR'</b>: -0.47</li>
<li><b>'CH3-SR'</b> or <b>'CH2sp3-SR'</b>: 0.235</li>
</ul>
</dt>
<dt>Disulfides (from <a href="../references.html#jorgensen_1986_sulfur">Jorgensen 1986 sulfur</a>)
<ul>
<li><b>'CH3-SR'</b> or <b>'CH2sp3-SR'</b>: 0.30</li>
<li><b>'S-RSR'</b>: -0.30</li>
<li><b>'S-RSR'</b>: -0.30</li>
<li><b>'CH3-SR'</b> or <b>'CH2sp3-SR'</b>: 0.30</li>
</ul>
</dt>
<dt>SH<sub>2</sub> (from <a href="../references.html#jorgensen_1986_sulfur">Jorgensen 1986 sulfur</a>)
<ul>
<li><b>'H'</b>: 0.235</li>
<li><b>'S-HSH'</b>: -0.47</li>
<li><b>'H'</b>: 0.235</li>
</ul>
</dt>
<dt>HF (from <a href="../references.html#cournoyer_jorgensen_1984">Cournoyer and Jorgensen 1984</a>)
<ul>
<li><b>'H'</b>: 0.64942</li>
<li><b>'F'</b>: -0.64942</li>
</ul>
</dt>
<dt>Parameters for Amides and Peptides (from <a href="../references.html#jorgensen_swenson_1985">Jorgensen and Swenson 1985</a>)
<ul>
<li><b>'Nsp2'</b> (1<sup>o</sup>) formamide, Asn: -0.85</li>
<li><b>'Nsp2'</b> (2<sup>o</sup>) NMA, Ala: -0.57</li>
<li><b>'Nsp2'</b> (3<sup>o</sup>) DMF, Pro: -0.57</li>
<li><b>'H'</b> (N1<sup>o</sup>) formamide, Asn: 0.425</li>
<li><b>'H'</b> (N2<sup>o</sup>) NMA, Ala: 0.37</li>
<li><b>'Osp2'</b> (C=O) amides: -0.50</li>
<li><b>'Csp2'</b> (C=O) NMA, Ala: 0.50</li>
<li><b>'CHsp2-N'</b> (CH=O) formamide: 0.50</li>
<li><b>'CH3-N'</b> (N2<sup>o</sup>) NMA: 0.20</li>
<li><b>'CH3-N'</b> (N3<sup>o</sup>) DMF: 0.285</li>
<li><b>'CH2sp3-N'</b> C<sub>alpha</sub> in Gly: 0.20</li>
<li><b>'CHsp3-N'</b> C<sub>alpha</sub> in Ala: 0.20</li>
<li><b>'CHsp3-N'</b> C<sub>alpha</sub> in Pro: 0.285</li>
<li><b>'CH2sp3-N'</b> Pro: 0.285</li>
<li><b>'CH3-N'</b> (C=O) NMA: 0.0</li>
</ul>
</dt>
<dt>Acetonitrile (from <a href="../references.html#jorgensen_briggs_1988">Jorgensen and Briggs 1988</a>)
<ul>
<li><b>'CH3-C1'</b>: 0.15</li>
<li><b>'Csp'</b>: 0.28</li>
<li><b>'Ns'</b>: -0.43</li>
</ul>
</dt>
</ul>
<b>Improper torsions</b>
<ul>
There are no improper torsions currently implemented for this force
field.
</ul>
<b>Proteins</b>
<ul>
The protein builder is not implemented for this force field.
</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 -->September 07, 2005<!-- #EndDate -->
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