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<title>MCCCS Towhee (OPLS-2001)</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-2001)</font></b> </font> </div>
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<td width="697" valign="top"> <b>Overview</b>
<ul>
This section covers the OPLS-2001 force field as it is implemented into the towhee_ff_OPLS-2001 file in the
ForceFields directory. All of the Towhee atom types for the OPLS-2001 force field
are listed, along with a short description of their meanings. For more
information about the OPLS force fields see the <a href="http://zarbi.chem.yale.edu/">Jorgensen
group home page</a>. Note that OPLS-2001 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-2001 was preceeded by a united-atom version of the force field
called <a href="oplsua.html">OPLS-ua</a> and an earlier version of the all-atom force field
called <a href="oplsaa.html">OPLS-aa</a>.
I would like to acknowledge W.L. Jorgensen for kindly providing me with
an electronic copy of the OPLS-2001 parameters. Any discrepencies (especially
typos) from the published OPLS-2001 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-2001</b>
<ul>
OPLS-2001 was implemented acording to an electronic file available from the Jorgensen group, but the
official reference is also listed below.
<ul>
<li><a href="../references.html#jorgensen_per_com_2001">Jorgensen <i>personal communication</i> 2001</a></li>
<li><a href="../references.html#kaminski_et_al_2001">Kaminski <i>et al.</i> 2001</a></li>
</ul>
</ul>
<b>OPLS-2001 in Towhee</b>
<ul>
The official force field name for OPLS-2001 in Towhee is 'OPLS-2001'. Here
I list all of the OPLS-2001 atom names for use in the towhee_input file,
along with a brief description taken from the OPLS-2001 literature. Notice
that OPLS-2001 uses almost the same naming conventions as the Amber param96
force field. This is not a coincedence as these force fields utilize many
of the same bonded interaction terms. I have modified some of the atom
names from the standard OPLS-2001 in order to create unique type names.
This was needed because OPLS-2001 occasionally uses different bonded interactions
for atoms which have the same atom name for nonbonded interactions. I
do not always distinguish between the original OPLS-2001 comments, and my
modifications as I have created several new atom names. Some of my comments
are placed 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">Bromine</font></dt>
<li><b>'Br-'</b> : bromine ion (charge -1)[uses the parameters from
the LGM force field]</li>
<dt><font color="red">Carbon</font></dt>
<li><b>'C a'</b> : carbon in O-C=O acid</li>
<li><b>'C k'</b> : carbon in C=O not bonded to N, and not an acid group
</li>
<li><b>'C n'</b> : carbon in N-C=O</li>
<li><b>'C*'</b> : aromatic C in 5-membered ring next to two carbons</li>
<li><b>'CA~'</b> : neutral aromatic carbon not at the junction of 5-membered
and 6-membered rings</li>
<li><b>'CA+'</b> : aromatic carbon in guanidinium C+</li>
<li><b>'CAj'</b> : neutral aromatic carbon at the juction of 5-membered
and 6-membered rings</li>
<li><b>'CAxna'</b> : special parameters for nucleotide bases. aromatic
C in DAP C2,C3,C4 pyridine; Cytosine C4,C5,C6</li>
<li><b>'CBxna'</b> : special parameters for nucleotide bases. Adenine
C4,C5,C6; Guanine C2,C4,C5</li>
<li><b>'CB'</b> : aromatic C at juntion of 5-membered and 6-membered
rings</li>
<li><b>'CKxna'</b> : special parameters for nucleotide bases. Adenine
C8 Guanine</li>
<li><b>'C='</b> : alkene sp<sup>2</sup> carbon (non-aromatic) interior carbons in a diene.</li>
<li><b>'CM'</b> : alkene sp<sup>2</sup> carbon (non-aromatic)</li>
<li><b>'CMxna'</b> : special parameters for nucleotide bases. Carbon
in Uracil C5,C6</li>
<li><b>'CO'</b> : sp<sup>3</sup> anomeric carbon (bonded to ether O
and alcohol O). this type shows up in carbohydrates</li>
<li><b>'CQ'</b> : sp<sup>2</sup>C in 6-membered ring between deprotonated
N's </li>
<li><b>'CR'</b> : aromatic C in 5-membered ring next to two nitrogens</li>
<li><b>'CS'</b> : aromatic C which does not have 120 degree bond angles
with all of its neighbors. Examples are C3 in pyrrole and C3 in furan</li>
<li><b>'CT'</b> : aliphatic sp<sup>3</sup> hybrid carbon</li>
<li><b>'CTf'</b> : aliphatic sp<sup>3</sup> hybrid carbon bonded to
F (monoalkyl fluorides and perfluoroalkanes)</li>
<li><b>'CTcf4'</b> : aliphatic sp<sup>3</sup> hybrid carbon bonded to
F in CF4</li>
<li><b>'CTxna'</b> : special parameters for nucleotide bases. Thymine
C-C5, 9-Me A or G C-N9</li>
<li><b>'CU'</b> : aromatic C which abuts NB in a heteroatom-heteroatom
bond. Examples are C3 in pyrazole and C3 in isoxazole</li>
<li><b>'CV'</b> : aromatic C in 5-membered ring next to C and deprotonated
N</li>
<li><b>'CW'</b> : sp<sup>2</sup> aromatic C in 5-membered ring next
to C and NH</li>
<dt><font color="red">Chlorine</font></dt>
<li><b>'Cl'</b> : chlorine bonded to a carbon</li>
<li><b>'Cl-'</b> : chlorine ion (charge -1)</li>
<dt><font color="red">Fluorine</font></dt>
<li><b>'F'</b> : fluorine nonionic (monoalkyl fluorides)</li>
<li><b>'Fpf'</b> : fluorine nonionic (perfluoroalkanes)</li>
<li><b>'F-'</b> : fluorine ion (charge -1)</li>
<dt><font color="red">Hydrogen</font></dt>
<li><b>'H'</b> : H attached to N</li>
<li><b>'H2xna'</b> : special parameters for nucleotide bases. DAP H-amine,
Cytosine, Adenine</li>
<li><b>'HA'</b> : H bonded to an aromatic ring</li>
<li><b>'HC~1'</b> : hydrogen attached to an sp<sup>3</sup> carbon in
most cases, see special cases of hydrogen below</li>
<li><b>'HC~2'</b> : H bonded to a non-aromatic sp<sup>2</sup> carbon
which is not bonded to a N, not double bonded to O, and is not bonded
to C=O</li>
<li><b>'HC~3'</b> : H bonded to a C=O or bonded to a C which is bonded
to a C=O</li>
<li><b>'HC~4'</b> : H bonded to a CT that is bonded to NT</li>
<li><b>'HCxna'</b> : special parameters for nucleotide bases. DAP H3,H4;
Uracil H-C5,H-C6; Thymine H-CC5; Cytosine H-C5,H-C6; Adenine H-C2,H-C8;
Guanine</li>
<li><b>'HO'</b> : H attached to O in alcohol</li>
<li><b>'HS'</b> : H attached to S</li>
<li><b>'HW'</b> : H on TIP3P, TIP4P or TIP5P water</li>
<dt><font color="red">Iodine</font></dt>
<li><b>'I-'</b> : iodine ion (charge -1)</li>
<dt><font color="red">Lithium</font></dt>
<li><b>'Li+'</b> : lithium ion (charge +1)</li>
<dt><font color="red">Nitrogen</font></dt>
<li><b>'N'</b> : N in an amide</li>
<li><b>'N2'</b> : sp<sup>2</sup> N of aromatic amines and guanidinium
ions</li>
<li><b>'NA'</b> : sp<sup>2</sup> aromatic N with H attached</li>
<li><b>'NB'</b> : sp<sup>2</sup> N in 5-membered ring, deprotonated</li>
<li><b>'NC'</b> : sp<sup>2</sup> N in 6-membered ring, deprotonated</li>
<li><b>'NO'</b> : sp<sup>2</sup> N in a nitro group</li>
<li><b>'NT~1'</b> : sp<sup>3</sup> N in ammonia</li>
<li><b>'NT+1'</b> : sp<sup>3</sup> N in ammonium ion (charge +1)</li>
<li><b>'NT~2'</b> : sp<sup>3</sup> N in primary, secondary, tertiary
amine</li>
<li><b>'NT+2'</b> : sp<sup>3</sup> N in primary, secondary, tertiary
ammonium ion (charge +1)</li>
<dt><font color="red">Oxygen</font></dt>
<li><b>'O'</b> : oxygen in C=O, not an acidic site</li>
<li><b>'O2'</b> : oxygen double bonded to carbon in COO- or COOH</li>
<li><b>'OHa'</b> : oxygen bonded to H in RCOOH</li>
<li><b>'OHm'</b> : oxygen bonded to H in a mono-alcohol</li>
<li><b>'OHp'</b> : oxygen bonded to H in polyols or phenol</li>
<li><b>'OHd'</b> : oxygen bonded to H in diols</li>
<li><b>'OHt'</b> : oxygen bonded to H in triols</li>
<li><b>'OS'</b> : sp<sup>3</sup> O in an ether or acetal</li>
<li><b>'OWt3p'</b> : water oxygen in the TIP3P model </li>
<li><b>'OWt4p'</b> : water oxygen in the TIP4P model</li>
<li><b>'OWt5p'</b> : water oxygen in the TIP5P model</li>
<li><b>'L4p'</b> : negative charge site on the TIP4P water</li>
<li><b>'L5p'</b> : negative charge sites on the TIP5P water</li>
<dt><font color="red">Sodium</font></dt>
<li><b>'Na+'</b> : sodium ion (charge +1)</li>
<dt><font color="red">Sulfur</font></dt>
<li><b>'S'</b> : S in sulfide, disulfide</li>
<li><b>'SH'</b> : S in thiols</li>
</ul>
</ul>
<b>Coulombic interactions</b>
<ul>
OPLS-2001 uses atom-centered point charges to represent the electrostatic interactions.
I do not know of an automated way to assign these point charges. Instead, you need to
consult the <a href="../references.html#force_fields_opls">OPLS-2001 literature</a>, or
(even better) ask the Jorgensen group for a copy of the force field file, and then find
molecules with similar moieties to the ones on the molecule you wish to simulate.
</ul>
<b>Improper torsions</b>
<ul>
OPLS-2001 uses stereocenter improper torsions to enforce planarity in aromatic rings,
around amide nitrogens, and around other sp2 carbons. 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>
OPLS-2001 has a complete parameter set for proteins, but I have not yet
implemented this into the protein builder. It is on my list of things
to do, but is not a high priority at the moment. If someone else would
like to add it into the builder I would be happy to provide advice about
how to perform that task. Note that since the OPLS-aa protein builder is
implemented, only minor changes would be needed to implement OPLS 2001
(the primary difference is the amino-acid-specific torsions).
</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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