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<title>MCCCS Towhee (OPLS-aa)</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-aa)</font></b> </font> </div>
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<td width="697" valign="top"> <b>Overview</b>
<ul>
This section covers the OPLS-aa force field as it is implemented into the towhee_ff_OPLS-aa file in the
ForceFields directory. All of the Towhee atom types for the OPLS-aa force field
are listed, along with a short description of their meanings. For more
information about the OPLS-aa force field see the <a href="http://zarbi.chem.yale.edu/">Jorgensen
group home page</a>. Note that OPLS-aa 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-aa was preceded by a united-atom version of the force field
called <a href="oplsua.html">OPLS-ua</a>
and has been reparameterized into what I call <a href="opls2001.html">OPLS-2001</a>.
I would like to acknowledge W.L. Jorgensen for kindly providing me with
an electronic copy of the OPLS-aa parameters. Any discrepencies (especially
typos) from the published OPLS-aa 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-aa</b>
<ul>
OPLS-aa 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#pranata_et_al_1991">Pranata <i>et al.</i> 1991</a></li>
<li><a href="../references.html#kaminski_et_al_1994">Kaminski <i>et al.</i> 1994</a></li>
<li><a href="../references.html#jorgensen_et_al_1996">Jorgensen <i>et al.</i> 1996</a></li>
<li><a href="../references.html#jorgensen_per_com_1996">Jorgensen <i>personal communication</i> 1996</a></li>
<li><a href="../references.html#damm_et_al_1997">Damm <i>et al.</i> 1997</a></li>
<li><a href="../references.html#jorgensen_mcdonald_1998">Jorgensen and McDonald 1998</a></li>
<li><a href="../references.html#mcdonald_jorgensen_1998">McDonald and Jorgensen 1998</a></li>
<li><a href="../references.html#mcdonald_et_al_1998">McDonald <i>et al</i> 1998</a></li>
<li><a href="../references.html#rizzo_jorgensen_1999">Rizzo and Jorgensen 1999</a></li>
<li><a href="../references.html#jorgensen_per_com_2001">Jorgensen <i>personal communication</i> 2001</a></li>
</ul>
</ul>
<b>OPLS-aa in Towhee</b>
<ul>
The official force field name for OPLS-aa in Towhee is 'OPLS-aa'. Here
I list all of the OPLS-aa atom names for use in the towhee_input file,
along with a brief description taken from the OPLS-aa literature. Notice
that OPLS-aa 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-aa in order to create unique type names.
This was needed because OPLS-aa 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-aa 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>'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>'CN'</b> : aromatic carbon in tryptophan at position CE2.</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</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 </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>
<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>'N3~'</b> : sp<sup>3</sup> neutral N of amines. NOTE: the N3
parameters are obsoleted by the NT parameters. I have included them
here in case you want to study these older parameters, but I would
recomend using the NT versions.</li>
<li><b>'N3+'</b> : sp<sup>3</sup> N ammonium ions (charge +1). NOTE:
the N3 parameters are obsoleted by NT parameters. I have included
them here in case you want to study these older parameters, but I
would recomend using the NT versions.</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>'OS'</b> : sp<sup>3</sup> O in an ether or acetal</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-aa 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
look through the <a href="../references.html#force_fields_opls">OPLS-aa literature</a> to find
molecules with similar moieties to the ones on the molecule you wish to simulate.
</ul>
<b>Improper torsions</b>
<ul>
OPLS-aa 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). Improper torsions for proteins are exactly the same as implemented in
AMBER96 - even though OPLS puts the stereocenter in the second position of the torsion,
you still define them in towhee putting it in the first position (towhee automatically
adjusts the parameter order for you).
</ul>
<b>Proteins</b>
<ul>
The OPLS-aa protein builder has been implemented with all charges verbatim from WLJ 1996.
(Note that the sidechain charges on Met and Cys were later revised in OPLS-2001). Because many
of the bonded parameters are unpublished, they have been cobbled together from other OPLS-aa
implementations, namely ffoplsaabon.itp in GROMACS 3.2.1 and oplsaa.prm in TINKER 4.0- the origin
of added parameters is referenced in the comments of ffoplsaa.F. Most of the missing parameters merely
required additional aliases to existing entries because of the above naming convention. Note that
GROMACS uses nanometers and KJoules instead of Angstroms and Kcals so
<a href="http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/1358.html">
unit conversions</a> are necessary when comparing Towhee and GROMACS results.
Here is a complete list of the codes for the 20 amino acids, plus some other functional
groups that work with the protein builder.
<ul>
<li>'a0' alanine</li>
<li>'c0' cysteine with hydrogen on the sulfur</li>
<li>'cs' cysteine in a disulfide bond</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. Despite a great deal of effort this amino acid is still not working properly with this
forcefield as there are many parameters that are missing. You will get an error if you include this
amino acid for this forcefield.
</li>
<li>'y0' tyrosine</li>
<li>'za' acetyl cap on the N-terminus</li>
<li>'zm' amide cap (NH<sub>2</sub>) on the C-terminus.</li>
<li>'zn' N-methylamide cap on the C-terminus</li>
<li>'zf' formaldahyde cap on the N-terminus</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 -->June 28, 2006<!-- #EndDate -->
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