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<div align="center"> <font size="5"> <b><font face="Arial, Helvetica, sans-serif"><a name="top"></a>MCCCS
Towhee (Charmm27)</font></b> </font> </div>
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<td width="697" valign="top"> <b>Overview</b>
<ul>
This section covers the Charmm27 force field as it is implemented into the
towhee_ff_Charmm27 file in the ForceFields directory.
All of the Towhee atom types for the Charmm27 force field
are listed, along with a short description of their meanings.
Charmm27 is a Lennard-Jones (12-6) force field and typically uses
the Lorentz-Berthelot mixing rules. Any discrepencies
(especially typos) from the published Charmm27 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 Charmm27</b>
<ul>
The best literature references for the Charmm27 forcefield parameters are
<ul>
<li><a href="../references.html#foloppe_mackerell_2000">Foloppe and MacKerell 2000</a></li>
</ul>
and
<ul>
<li><a href="../references.html#mackerell_et_al_1998">MacKerell <i> et al.</i> 1998</a>.</li>
</ul>
There are parameter (par_all27_prot_na.inp) and topology (top_all27_prot_na.inp) files
that are extremely helpful, and can be found on
<a href="http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm">Alex MacKerell's force field web
site</a>. There is also a forum for Charmm discussion at <a href="http://www.charmm.org">Charmm.org</a>.
</ul>
<b>Charmm27 in Towhee</b>
<ul>
The official force field name for Charmm27 in Towhee is 'Charmm27'. Here I list all
of the Charmm27 atom names for use in the towhee_input file, along with a brief
description.
Please note that the capitalization and spacing pattern is important
and must be followed exactly as listed here.
<ul>
<dt><font color="red">Calcium</font></dt>
<li><b>'CAL'</b> : Calcium ion</li>
<dt><font color="red">Carbon</font></dt>
<li><b>'C'</b> : Carbonyl carbon, peptide backbone </li>
<li><b>'CA'</b> : Aromatic carbon</li>
<li><b>'CC'</b> : Carbonyl carbon (in Asn, Asp, Gln, Glu, and C terminal)</li>
<li><b>'CD'</b> : Carbonyl carbon (in protonated Glu and Asp)</li>
<li><b>'CE1'</b> : Carbon in alkene (R-CH=CH-R) non-lipid version. This is essentially the same as the
<b>CEL1</b> term as Charmm27 has some redundancy in its naming conventions.</li>
<li><b>'CE2'</b> : Carbon in ethene (CH2=CH2) non-lipid version. This is essentially the same as the
<b>CEL2</b> term as Charmm27 has some redundancy in its naming conventions.</li>
<li><b>'CEL1'</b> : Carbon in alkene (R-CH=CH-R) lipid. This is essentially the same as the
<b>CE1</b> term as Charmm27 has some redundancy in its naming conventions.</li>
<li><b>'CEL2'</b> : Carbon in ethene (CH2=CH2) lipid version. This is essentially the same as the
<b>CE2</b> term as Charmm27 has some redundancy in its naming conventions.</li>
<li><b>'CL'</b> : Methyl Acetate update.</li>
<li><b>'CM'</b> : Heme CO carbon</li>
<li><b>'CN1'</b> : Carbonyl carbon (Nucleic Acids)</li>
<li><b>'CN1A'</b> : NAD+/NADH amide carbonyl carbon (Nucleic Acids)</li>
<li><b>'CN1T'</b> : Carbonyl carbon for thymine/uridine C2 (Nucleic Acids)</li>
<li><b>'CN2'</b> : Aromatic carbon to amide (Nucleic Acids)</li>
<li><b>'CN3'</b> : Aromatic carbon (Nucleic Acids)</li>
<li><b>'CN3A'</b> : Aromatic carbon for NAD+ (Nucleic Acids)</li>
<li><b>'CN3B'</b> : Aromatic carbon for NAD+ (Nucleic Acids)</li>
<li><b>'CN3C'</b> : Aromatic carbon for NADH (Nucleic Acids)</li>
<li><b>'CN3D'</b> : Aromatic carbon for 5-methylcytosine (Nucleic Acids)</li>
<li><b>'CN3T'</b> : Aromatic carbon for thymine C5 (Nucleic Acids)</li>
<li><b>'CN4'</b> : Carbon for purine C8 and ADE C2 (Nucleic Acids)</li>
<li><b>'CN5'</b> : Carbon for purine C4 and C5 (Nucleic Acids)</li>
<li><b>'CN5G'</b> : Carbon for quanine C5 (Nucleic Acids)</li>
<li><b>'CN7'</b> : Aliphatic sp3 carbon for CH (equivalent to protein CT1) (Nucleic Acids)</li>
<li><b>'CN7B'</b> : Aliphatic carbon for C1' (Nucleic Acids)</li>
<li><b>'CN7C'</b> : Carbon for C2' in arabinose (Nucleic Acids)</li>
<li><b>'CN7D'</b> : Carbon for C2' in nucleic acid fluorine derivatives (Nucleic Acids)</li>
<li><b>'CN8'</b> : Aliphatic sp3 carbon for CH2 (equivalent to protein CT2) (Nucleic Acids)</li>
<li><b>'CN8B'</b> : Aliphatic sp3 carbon for CH2 (equivalent to protein CT2) (Nucleic Acids)</li>
<li><b>'CN9'</b> : Aliphatic sp3 carbon for CH3 (equivalent to protein CT3) (Nucleic Acids)</li>
<li><b>'CNA'</b> : Pure aromatic carbon (Nucleic Acids)</li>
<li><b>'CNA2'</b> : Pure aromatic carbon bound to fluorine (Nucleic Acids)</li>
<li><b>'CNE1'</b> : Carbon in alkene (RHC=CR) (Nucleic Acids)</li>
<li><b>'CNE2'</b> : Carbon in alkene (H2C=CR) (Nucleic Acids)</li>
<li><b>'CP1'</b> : Tetrahedral carbon (proline CA)</li>
<li><b>'CP2'</b> : Tetrahedral carbon (proline CB/CG)</li>
<li><b>'CP3'</b> : Tetrahedral carbon (proline CD)</li>
<li><b>'CPA'</b> : Heme alpha-carbon</li>
<li><b>'CPB'</b> : Heme beta-carbon</li>
<li><b>'CPH1'</b> : Histidine CG and CD2 carbons</li>
<li><b>'CPH2'</b> : Histidine CE1 carbon</li>
<li><b>'CPM'</b> : Heme meso-carbon</li>
<li><b>'CPT'</b> : Tryptophan carbon between rings</li>
<li><b>'CS'</b> : Thiolate carbon</li>
<li><b>'CT1'</b> : Aliphatic sp<sup>3</sup> carbon for CH non-lipid version</li>
<li><b>'CT2'</b> : Aliphatic sp<sup>3</sup> carbon for CH2 non-lipid version</li>
<li><b>'CT3'</b> : Aliphatic sp<sup>3</sup> carbon for CH3 non-lipid version</li>
<li><b>'CTL1'</b> : Aliphatic sp<sup>3</sup> carbon for CH lipid version</li>
<li><b>'CTL2'</b> : Aliphatic sp<sup>3</sup> carbon for CH2 lipid version</li>
<li><b>'CTL3'</b> : Aliphatic sp<sup>3</sup> carbon for CH3 lipid version</li>
<li><b>'CTL5'</b> : tetramethylammonium</li>
<li><b>'CY'</b> : Tryptophan carbon in pyrole ring</li>
<dt><font color="red">Cesium</font></dt>
<li><b>'CES'</b> : Cesium ion</li>
<dt><font color="red">Chlorine</font></dt>
<li><b>'CLA'</b> : Chlorine ion</li>
<dt><font color="red">Fluorine</font></dt>
<li><b>'FA1'</b> : Aromatic fluorine</li>
<li><b>'FN1'</b> : Fluorine for sugar derivatives</li>
<dt><font color="red">Hydrogen</font></dt>
<li><b>'H'</b> : Polar hydrogen</li>
<li><b>'HA'</b> : Nonpolar hydrogen</li>
<li><b>'HAL1'</b> : Nonpolar hydrogen in a lipid, bonded to <b>CTL1</b></li>
<li><b>'HAL2'</b> : Nonpolar hydrogen in a lipid, bonded to <b>CTL2</b></li>
<li><b>'HAL3'</b> : Nonpolar hydrogen in a lipid, bonded to <b>CTL3</b></li>
<li><b>'HB'</b> : Backbone hydrogen</li>
<li><b>'HC'</b> : Hydrogen in N terminal group</li>
<li><b>'HCL'</b> : Hydrogen in ethanolamine</li>
<li><b>'HE1'</b> : Hydrogen in alkene (RHC=CR)</li>
<li><b>'HE2'</b> : Hydrogen in alkene (H2C=CR)</li>
<li><b>'HEL1'</b> : Hydrogen in alkene (lipid version) bonded to <b>CEL1</b></li>
<li><b>'HEL2'</b> : Hydrogen in alkene (lipid version) bonded to <b>CEL2</b></li>
<li><b>'HL'</b> : Polar hydrogen on NC4+</li>
<li><b>'HN1'</b> : Amine proton (Nucleic Acids)</li>
<li><b>'HN2'</b> : Ring nitrogen proton (Nucleic Acids)</li>
<li><b>'HN3'</b> : Aromatic carbon proton (Nucleic Acids)</li>
<li><b>'HN3B'</b> : NAD+ aromatic hydrogen (Nucleic Acids)</li>
<li><b>'HN3C'</b> : Standard aromatic hydrogen (as in benzene) (Nucleic Acids)</li>
<li><b>'HN4'</b> : Phosphate hydroxyl proton (Nucleic Acids)</li>
<li><b>'HN5'</b> : Ribose hydroxyl proton (Nucleic Acids)</li>
<li><b>'HN6'</b> : Ribose aliphatic proton (Nucleic Acids)</li>
<li><b>'HN7'</b> : Nonpolar hydrogen (equivalent to protein HA) (Nucleic Acids)</li>
<li><b>'HN8'</b> : Hydrogen bound to CN8 in nucleic acids/model compounds (Nucleic Acids)</li>
<li><b>'HN9'</b> : Hydrogen bound to CN9 in nucleic acids/model compounds (Nucleic Acids)</li>
<li><b>'HNE1'</b> : Hydrogen in alkene (RHC=CR) (Nucleic Acids)</li>
<li><b>'HNE2'</b> : Hydrogen in alkene (H2C=CR) (Nucleic Acids)</li>
<li><b>'HNP'</b> : Pure aromatic hydrogen (Nucleic Acids)</li>
<li><b>'HOL'</b> : Hydrogen bondd to oxygen in acetic acid</li>
<li><b>'HP'</b> : Aromatic hydrogen</li>
<li><b>'HR1'</b> : Histidine HE1 hydrogen, (+)-charged histidine HG and HD2 hydrogens </li>
<li><b>'HR2'</b> : (+)-charged histidine HE1 hydrogen </li>
<li><b>'HR3'</b> : Histidine HG and HD2 hydrogens </li>
<li><b>'HS'</b> : Thiol hydrogen</li>
<li><b>'HT'</b> : Water hydrogen, modified TIP3P model</li>
<dt><font color="red">Iron</font></dt>
<li><b>'FE'</b> : Iron in heme</li>
<dt><font color="red">Magnesium</font></dt>
<li><b>'MG'</b> : Magnesium ion</li>
<dt><font color="red">Nitrogen</font></dt>
<li><b>'N'</b> : Proline nitrogen</li>
<li><b>'NC2'</b> : Guanidinium nitrogen</li>
<li><b>'NH1'</b> : Peptide nitrogen</li>
<li><b>'NH2'</b> : Amide nitrogen</li>
<li><b>'NH3'</b> : Ammonium nitrogen</li>
<li><b>'NH3L'</b> : Ethanolamine nitrogen</li>
<li><b>'NN1'</b> : Amide nitrogen (Nucleic Acids)</li>
<li><b>'NN1C'</b> : Imine nitrogen (cytosine) (Nucleic Acids)</li>
<li><b>'NN2'</b> : Protonated ring nitrogen (Nucleic Acids)</li>
<li><b>'NN2B'</b> : For N9 in guanine (Nucleic Acids)</li>
<li><b>'NN2C'</b> : Protonated ring nitrogen (cytosine) (Nucleic Acids)</li>
<li><b>'NN2G'</b> : Protonated ring nitrogen for guanine N1 (Nucleic Acids)</li>
<li><b>'NN2U'</b> : Protonated ring nitrogen for uridine N3 (Nucleic Acids)</li>
<li><b>'NN3'</b> : Unprotonated ring nitrogen (Nucleic Acids)</li>
<li><b>'NN3A'</b> : Unprotonated ring nitrogen for adenine N1 and N3 (Nucleic Acids)</li>
<li><b>'NN3G'</b> : Unprotonated ring nitrogen for guanine N3 (Nucleic Acids)</li>
<li><b>'NN3I'</b> : Unprotonated ring nitrogen for inosine N3 (Nucleic Acids)</li>
<li><b>'NN4'</b> : Nitrogen for purine N7 (Nucleic Acids)</li>
<li><b>'NN5'</b> : sp2 amine nitrogen (Nucleic Acids)</li>
<li><b>'NN6'</b> : sp3 amine nitrogen (equivalent to protein NH3) (Nucleic Acids)</li>
<li><b>'NP'</b> : Proline ring NH2+</li>
<li><b>'NPH'</b> : Heme pyrole nitrogen</li>
<li><b>'NR1'</b> : Neutral histidine protonated ring nitrogen</li>
<li><b>'NR2'</b> : Neutral histidine unprotonated ring nitrogen</li>
<li><b>'NR3'</b> : (+)-charged histidine ring nitrogen</li>
<li><b>'NTL'</b> : tetramethyl ammonium</li>
<li><b>'NY'</b> : Tryptophan nitrogen in pyrole ring</li>
<dt><font color="red">Oxygen</font></dt>
<li><b>'O'</b> : Carbonyl oxygen</li>
<li><b>'O2L'</b> : Oxygen in sulfate or phosphate</li>
<li><b>'OB'</b> : Carbonyl oxygen in acetic acid non-lipid version</li>
<li><b>'OBL'</b> : Carbonyl oxygen in acetic acid lipid version</li>
<li><b>'OC'</b> : Carboxylate oxygen non-lipid version</li>
<li><b>'OCL'</b> : Carboxylate oxygen lipid version</li>
<li><b>'OH1'</b> : Hydroxyl oxygen non-lipid version</li>
<li><b>'OHL'</b> : Hydroxyl oxygen lipid version</li>
<li><b>'OM'</b> : Heme CO/O2 oxygen</li>
<li><b>'ON1'</b> : Carbonyl oxygen (Nucleic Acids)</li>
<li><b>'ON1C'</b> : Carbonyl oxygen for cytosine O2 (Nucleic Acids)</li>
<li><b>'ON2'</b> : Phosphate ester oxygen (Nucleic Acids)</li>
<li><b>'ON3'</b> : Double bonded oxygen in phospate (Nucleic Acids)</li>
<li><b>'ON4'</b> : Phospate hydroxyl oxygen (Nucleic Acids)</li>
<li><b>'ON5'</b> : Ribose hydroxyl oxygen (Nucleic Acids)</li>
<li><b>'ON6'</b> : Deoxyribose ring oxygen (Nucleic Acids)</li>
<li><b>'ON6B'</b> : Ribose ring oxygen (Nucleic Acids)</li>
<li><b>'OS'</b> : Ester oxygen non-lipid version</li>
<li><b>'OSL'</b> : Ester oxygen lipid version</li>
<li><b>'OT'</b> : Water oxygen, modified TIP3P model</li>
<dt><font color="red">Phosphorous</font></dt>
<li><b>'P'</b> : Phosphorous non-lipid version</li>
<li><b>'P2'</b> : Pyrophosphate phosphorous</li>
<li><b>'PL'</b> : Phosphorous lipid version</li>
<dt><font color="red">Potassium</font></dt>
<li><b>'POT'</b> : Potassium ion</li>
<dt><font color="red">Sodium</font></dt>
<li><b>'SOD'</b> : Sodium ion</li>
<dt><font color="red">Sulfur</font></dt>
<li><b>'S'</b> : Sulfur</li>
<li><b>'SL'</b> : Sulfur in sulfate</li>
<li><b>'SM'</b> : Sulfur (C-S-S-C type)</li>
<li><b>'SS'</b> : Thiolate sulfur</li>
</ul>
</ul>
<b>Coulombic Interactions</b>
<ul>
Charmm27 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 Charmm27. 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. Charmm27 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 Charmm27 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 Charmm27.
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 and the thiol and disulfide forms of cysteine) are
functional for the Charmm27 force field. I have implemented
the atom types and charges according to the published Charmm27
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.
<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</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. Note: differs from official Charmm27 by
having a 0.31 charge on both terminal H instead of giving one 0.30 and the other 0.32.</li>
<li>'zn' N-methylamide cap on the C-terminus</li>
</ul>
</ul>
<b>Nucleic acids</b>
<ul>
All of the basic nucleic acids are functional for the Charmm27 force field. I have implemented the atom types and charges according to the
published Charmm27 values. Below is a complete list of the codes for the nucleic acids. Notice that there is a 'd' as the first character
in the codes for the deoxyribonucleotides (used in DNA) and no 'd' in the codes for the ribonucleotides (used in RNA). Generally, thymine is
only found in DNA and uridine is only found in RNA, but both the deoxyribonucleotides and the ribonucleotides are implemented here.
The shortname is also provided (in parenthesis) for use with the buildpartial features.
.
<ul>
<li>'A' adenosine (AMP)</li>
<li>'dA' deoxyadenosine (dAMP)</li>
<li>'C' cytidine (CMP)</li>
<li>'dC' deoxycytidine (dCMP)</li>
<li>'G' guanosine (GUA)</li>
<li>'dG' deoxyguanosine (dGUA)</li>
<li>'T' thymidine (TMP)</li>
<li>'dT' deoxythymidine (dTMP)</li>
<li>'U' uridine (UMP)</li>
<li>'dU' deoxyuridine (dUMP)</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 -->October 17, 2006<!-- #EndDate -->
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