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<title>MCCCS Towhee (C19sasa)</title>
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<div align="center"> <font size="5"> <b><font face="Arial, Helvetica, sans-serif"><a name="top"></a>MCCCS
Towhee (C19sasa)</font></b> </font> </div>
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<td width="697" valign="top"> <b>Overview</b>
<ul>
This section covers the C19sasa force field (which is a
modified version of Charmm19 that includes an implicit
solvent model based on the solvent accessible surface area (SASA))
as it is implemented into the towhee_ff_c19sasa
file in the ForceFields directory. All of the Towhee atom
types for the C19sasa force field are listed, along with a
short description of their meanings. Note that Charmm19 uses a
'12-6 plus solvation' classical_potential and 'explicit' classical_mixrule
so it cannot currently be combined with any other forcefields. The implicit
water solvation is toggled on and off using the <b>isolvtype</b>
variable in the towhee_input file. Any
discrepencies (especially typos) from the published C19sasa
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 C19sasa</b>
<ul>
The best literature reference for the C19sasa forcefield parameters is
<ul>
<li><a href="../references.html#neria_et_al_1996">Neria <i>et al.</i> 1996</a></li>
</ul>
The best literature reference for the C19sasa solvation parameters is
<ul>
<li><a href="../references.html#lazaridis_karplus_1999">Lazaridis and Karplus 1999</a></li>
</ul>
This forcefield also uses parameter (param19_eef1.inp) and topology (toph19_eef1.inp) files
which are extremely helpful, but are only available in the Charmm28 distribution.
</ul>
<b>C19sasa in Towhee</b>
<ul>
The official force field name for C19sasa in Towhee is 'C19sasa'. Here I list all of
the C19sasa atom names for use in the towhee_input file, along with a brief description. C19sasa
denotes extended-atom for cases where the hydrogens and the heavy element they are bonded to are all
lumped into a single interaction site.
Please note that the capitalization and spacing pattern is important
and must be followed exactly as listed here. I include the atom notes from the Neria paper.
<ul>
<li><b>'C'</b> : Carbonyl carbon</li>
<li><b>'CH1E'</b> : Extended aliphatic carbon with one hydrogen -CH- group</li>
<li><b>'CH2E'</b> : Extended aliphatic carbon with two hydrogens -CH<sub>2</sub>- group</li>
<li><b>'CH3E'</b> : Extended methyl terminal -CH<sub>3</sub> group</li>
<li><b>'CM'</b> : Carbon in carbon monoxide</li>
<li><b>'CR'</b> : 4-bonded carbon in aromatics and Arginine</li>
<li><b>'CR1E'</b> : Extended aromatic carbon with one hydrogen</li>
<li><b>'CT'</b> : aliphatic carbon</li>
<li><b>'Fe'</b> : Iron</li>
<li><b>'H'</b> : Polar hydrogen</li>
<li><b>'HC'</b> : Polar hydrogen (in Arg, Lys, and N term)</li>
<li><b>'HT'</b> : Water hydrogen, modified TIP3P model</li>
<li><b>'N'</b> : Nitrogen with no hydrogens</li>
<li><b>'NC2'</b> : Nitrogen bound to two hydrogens (in Arg.)</li>
<li><b>'NH1'</b> : Nitrogen bound to one hydrogen</li>
<li><b>'NH2'</b> : Nitrogen bound to two hydrogens</li>
<li><b>'NH3'</b> : Nitrogen bound to three hydrogens</li>
<li><b>'NP'</b> : Pyrole nitrogen</li>
<li><b>'NR'</b> : Nitrogen in an aromatic ring with no hydrogens</li>
<li><b>'O'</b> : Carbonyl oxygen</li>
<li><b>'OC'</b> : Carboxyl oxygen</li>
<li><b>'OH1'</b> : Hydroxyl oxygen</li>
<li><b>'OH2'</b> : ST2 water oxygen</li>
<li><b>'OM'</b> : Heme CO/O2 oxygen</li>
<li><b>'OS'</b> : Ester oxygen</li>
<li><b>'OT'</b> : Water oxygen, modified TIP3P model</li>
<li><b>'S'</b> : Sulfur</li>
<li><b>'SH1E'</b> : Extended sulfur with one hydrogen</li>
</ul>
</ul>
<b>Coulombic Interactions</b>
<ul>
C19sasa utilizes point charges on atomic centers to represent the charge distribution on a molecule. As far as I know,
there is no automated system for assigning the charges in C19sasa. However, C19sasa uses a neutral group approach for
most moities found in organic molecules. The charge distibution is similiar to that used in Charmm19, except the ionic side
chain amino acids are neutralized, and the specifics on how to do this can be found in Lazaridis and Karplus 1999.
Otherwise, it is fairly easy to scan through the example molecular charge distributions found in the files available at the
<a href="http://www.pharmacy.umaryland.edu/faculty/amackere/">MacKerell research web site</a> and determine
what charges to apply to the molecule you wish to simulate.
</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. C19sasa exclusively
uses the out-of-plane 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. These torsions
are listed in the C19sasa literature as i-j-k-l where the
angle is the dihedral between i-j-k and j-k-l. The bonding
pattern is not completely clear to me, but it appears that
either i or l is the central atom which is bonded to all three
of the other atoms, and none of the other three atoms are
bonded to each other. In the towhee_input file the improper
torsions is listed starting from the central atom and the
three other atoms are listed in the same order as C19sasa.
So, if the central atom is i, then the atoms are listed j, k,
l. If the central atom is l then the atoms are listed k, j,
i. 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)
are functional for the C19sasa force field. I have implemented the atom types and charges according to the published
C19sasa values. Below is a complete list of the codes for the 20 amino acids, plus some other functional groups that
work with the protein builder. C19sasa does not apply a torsion across all set of atoms connected by 3 bonds
in the amino acids. The torsions are explicitly listed for these systems in the polyc19eef1.F routine. I tried
to faithfully reproduce all of their energetics, but had to make some accomodations for tryptophan. They have
two torsions in tryptophan that span atoms that are not bonded together and I could not implement those into
Towhee without a major reworking of configuartional-bias.
<ul>
<li>'a0' alanine</li>
<li>'c0' cysteine with hydrogen on the sulfur</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 (no parameters for N-terminal or C-terminal 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>
<p> </p>
<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 -->May 18, 2010<!-- #EndDate -->
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