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MCCCS Towhee (Charmm27)

 

 

Overview
    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.

     

References for Charmm27 Charmm27 in Towhee
    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.
      Calcium
    • 'CAL' : Calcium ion
    • Carbon
    • 'C' : Carbonyl carbon, peptide backbone
    • 'CA' : Aromatic carbon
    • 'CC' : Carbonyl carbon (in Asn, Asp, Gln, Glu, and C terminal)
    • 'CD' : Carbonyl carbon (in protonated Glu and Asp)
    • 'CE1' : Carbon in alkene (R-CH=CH-R) non-lipid version. This is essentially the same as the CEL1 term as Charmm27 has some redundancy in its naming conventions.
    • 'CE2' : Carbon in ethene (CH2=CH2) non-lipid version. This is essentially the same as the CEL2 term as Charmm27 has some redundancy in its naming conventions.
    • 'CEL1' : Carbon in alkene (R-CH=CH-R) lipid. This is essentially the same as the CE1 term as Charmm27 has some redundancy in its naming conventions.
    • 'CEL2' : Carbon in ethene (CH2=CH2) lipid version. This is essentially the same as the CE2 term as Charmm27 has some redundancy in its naming conventions.
    • 'CL' : Methyl Acetate update.
    • 'CM' : Heme CO carbon
    • 'CN1' : Carbonyl carbon (Nucleic Acids)
    • 'CN1A' : NAD+/NADH amide carbonyl carbon (Nucleic Acids)
    • 'CN1T' : Carbonyl carbon for thymine/uridine C2 (Nucleic Acids)
    • 'CN2' : Aromatic carbon to amide (Nucleic Acids)
    • 'CN3' : Aromatic carbon (Nucleic Acids)
    • 'CN3A' : Aromatic carbon for NAD+ (Nucleic Acids)
    • 'CN3B' : Aromatic carbon for NAD+ (Nucleic Acids)
    • 'CN3C' : Aromatic carbon for NADH (Nucleic Acids)
    • 'CN3D' : Aromatic carbon for 5-methylcytosine (Nucleic Acids)
    • 'CN3T' : Aromatic carbon for thymine C5 (Nucleic Acids)
    • 'CN4' : Carbon for purine C8 and ADE C2 (Nucleic Acids)
    • 'CN5' : Carbon for purine C4 and C5 (Nucleic Acids)
    • 'CN5G' : Carbon for quanine C5 (Nucleic Acids)
    • 'CN7' : Aliphatic sp3 carbon for CH (equivalent to protein CT1) (Nucleic Acids)
    • 'CN7B' : Aliphatic carbon for C1' (Nucleic Acids)
    • 'CN7C' : Carbon for C2' in arabinose (Nucleic Acids)
    • 'CN7D' : Carbon for C2' in nucleic acid fluorine derivatives (Nucleic Acids)
    • 'CN8' : Aliphatic sp3 carbon for CH2 (equivalent to protein CT2) (Nucleic Acids)
    • 'CN8B' : Aliphatic sp3 carbon for CH2 (equivalent to protein CT2) (Nucleic Acids)
    • 'CN9' : Aliphatic sp3 carbon for CH3 (equivalent to protein CT3) (Nucleic Acids)
    • 'CNA' : Pure aromatic carbon (Nucleic Acids)
    • 'CNA2' : Pure aromatic carbon bound to fluorine (Nucleic Acids)
    • 'CNE1' : Carbon in alkene (RHC=CR) (Nucleic Acids)
    • 'CNE2' : Carbon in alkene (H2C=CR) (Nucleic Acids)
    • 'CP1' : Tetrahedral carbon (proline CA)
    • 'CP2' : Tetrahedral carbon (proline CB/CG)
    • 'CP3' : Tetrahedral carbon (proline CD)
    • 'CPA' : Heme alpha-carbon
    • 'CPB' : Heme beta-carbon
    • 'CPH1' : Histidine CG and CD2 carbons
    • 'CPH2' : Histidine CE1 carbon
    • 'CPM' : Heme meso-carbon
    • 'CPT' : Tryptophan carbon between rings
    • 'CS' : Thiolate carbon
    • 'CT1' : Aliphatic sp3 carbon for CH non-lipid version
    • 'CT2' : Aliphatic sp3 carbon for CH2 non-lipid version
    • 'CT3' : Aliphatic sp3 carbon for CH3 non-lipid version
    • 'CTL1' : Aliphatic sp3 carbon for CH lipid version
    • 'CTL2' : Aliphatic sp3 carbon for CH2 lipid version
    • 'CTL3' : Aliphatic sp3 carbon for CH3 lipid version
    • 'CTL5' : tetramethylammonium
    • 'CY' : Tryptophan carbon in pyrole ring
    • Cesium
    • 'CES' : Cesium ion
    • Chlorine
    • 'CLA' : Chlorine ion
    • Fluorine
    • 'FA1' : Aromatic fluorine
    • 'FN1' : Fluorine for sugar derivatives
    • Hydrogen
    • 'H' : Polar hydrogen
    • 'HA' : Nonpolar hydrogen
    • 'HAL1' : Nonpolar hydrogen in a lipid, bonded to CTL1
    • 'HAL2' : Nonpolar hydrogen in a lipid, bonded to CTL2
    • 'HAL3' : Nonpolar hydrogen in a lipid, bonded to CTL3
    • 'HB' : Backbone hydrogen
    • 'HC' : Hydrogen in N terminal group
    • 'HCL' : Hydrogen in ethanolamine
    • 'HE1' : Hydrogen in alkene (RHC=CR)
    • 'HE2' : Hydrogen in alkene (H2C=CR)
    • 'HEL1' : Hydrogen in alkene (lipid version) bonded to CEL1
    • 'HEL2' : Hydrogen in alkene (lipid version) bonded to CEL2
    • 'HL' : Polar hydrogen on NC4+
    • 'HN1' : Amine proton (Nucleic Acids)
    • 'HN2' : Ring nitrogen proton (Nucleic Acids)
    • 'HN3' : Aromatic carbon proton (Nucleic Acids)
    • 'HN3B' : NAD+ aromatic hydrogen (Nucleic Acids)
    • 'HN3C' : Standard aromatic hydrogen (as in benzene) (Nucleic Acids)
    • 'HN4' : Phosphate hydroxyl proton (Nucleic Acids)
    • 'HN5' : Ribose hydroxyl proton (Nucleic Acids)
    • 'HN6' : Ribose aliphatic proton (Nucleic Acids)
    • 'HN7' : Nonpolar hydrogen (equivalent to protein HA) (Nucleic Acids)
    • 'HN8' : Hydrogen bound to CN8 in nucleic acids/model compounds (Nucleic Acids)
    • 'HN9' : Hydrogen bound to CN9 in nucleic acids/model compounds (Nucleic Acids)
    • 'HNE1' : Hydrogen in alkene (RHC=CR) (Nucleic Acids)
    • 'HNE2' : Hydrogen in alkene (H2C=CR) (Nucleic Acids)
    • 'HNP' : Pure aromatic hydrogen (Nucleic Acids)
    • 'HOL' : Hydrogen bondd to oxygen in acetic acid
    • 'HP' : Aromatic hydrogen
    • 'HR1' : Histidine HE1 hydrogen, (+)-charged histidine HG and HD2 hydrogens
    • 'HR2' : (+)-charged histidine HE1 hydrogen
    • 'HR3' : Histidine HG and HD2 hydrogens
    • 'HS' : Thiol hydrogen
    • 'HT' : Water hydrogen, modified TIP3P model
    • Iron
    • 'FE' : Iron in heme
    • Magnesium
    • 'MG' : Magnesium ion
    • Nitrogen
    • 'N' : Proline nitrogen
    • 'NC2' : Guanidinium nitrogen
    • 'NH1' : Peptide nitrogen
    • 'NH2' : Amide nitrogen
    • 'NH3' : Ammonium nitrogen
    • 'NH3L' : Ethanolamine nitrogen
    • 'NN1' : Amide nitrogen (Nucleic Acids)
    • 'NN1C' : Imine nitrogen (cytosine) (Nucleic Acids)
    • 'NN2' : Protonated ring nitrogen (Nucleic Acids)
    • 'NN2B' : For N9 in guanine (Nucleic Acids)
    • 'NN2C' : Protonated ring nitrogen (cytosine) (Nucleic Acids)
    • 'NN2G' : Protonated ring nitrogen for guanine N1 (Nucleic Acids)
    • 'NN2U' : Protonated ring nitrogen for uridine N3 (Nucleic Acids)
    • 'NN3' : Unprotonated ring nitrogen (Nucleic Acids)
    • 'NN3A' : Unprotonated ring nitrogen for adenine N1 and N3 (Nucleic Acids)
    • 'NN3G' : Unprotonated ring nitrogen for guanine N3 (Nucleic Acids)
    • 'NN3I' : Unprotonated ring nitrogen for inosine N3 (Nucleic Acids)
    • 'NN4' : Nitrogen for purine N7 (Nucleic Acids)
    • 'NN5' : sp2 amine nitrogen (Nucleic Acids)
    • 'NN6' : sp3 amine nitrogen (equivalent to protein NH3) (Nucleic Acids)
    • 'NP' : Proline ring NH2+
    • 'NPH' : Heme pyrole nitrogen
    • 'NR1' : Neutral histidine protonated ring nitrogen
    • 'NR2' : Neutral histidine unprotonated ring nitrogen
    • 'NR3' : (+)-charged histidine ring nitrogen
    • 'NTL' : tetramethyl ammonium
    • 'NY' : Tryptophan nitrogen in pyrole ring
    • Oxygen
    • 'O' : Carbonyl oxygen
    • 'O2L' : Oxygen in sulfate or phosphate
    • 'OB' : Carbonyl oxygen in acetic acid non-lipid version
    • 'OBL' : Carbonyl oxygen in acetic acid lipid version
    • 'OC' : Carboxylate oxygen non-lipid version
    • 'OCL' : Carboxylate oxygen lipid version
    • 'OH1' : Hydroxyl oxygen non-lipid version
    • 'OHL' : Hydroxyl oxygen lipid version
    • 'OM' : Heme CO/O2 oxygen
    • 'ON1' : Carbonyl oxygen (Nucleic Acids)
    • 'ON1C' : Carbonyl oxygen for cytosine O2 (Nucleic Acids)
    • 'ON2' : Phosphate ester oxygen (Nucleic Acids)
    • 'ON3' : Double bonded oxygen in phospate (Nucleic Acids)
    • 'ON4' : Phospate hydroxyl oxygen (Nucleic Acids)
    • 'ON5' : Ribose hydroxyl oxygen (Nucleic Acids)
    • 'ON6' : Deoxyribose ring oxygen (Nucleic Acids)
    • 'ON6B' : Ribose ring oxygen (Nucleic Acids)
    • 'OS' : Ester oxygen non-lipid version
    • 'OSL' : Ester oxygen lipid version
    • 'OT' : Water oxygen, modified TIP3P model
    • Phosphorous
    • 'P' : Phosphorous non-lipid version
    • 'P2' : Pyrophosphate phosphorous
    • 'PL' : Phosphorous lipid version
    • Potassium
    • 'POT' : Potassium ion
    • Sodium
    • 'SOD' : Sodium ion
    • Sulfur
    • 'S' : Sulfur
    • 'SL' : Sulfur in sulfate
    • 'SM' : Sulfur (C-S-S-C type)
    • 'SS' : Thiolate sulfur
Coulombic Interactions
    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 MacKerell research web site and determine what charges to apply to the molecule you wish to simulate.
Improper torsions
    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 sp2 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).
Proteins
    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.
    • 'a0' alanine
    • 'c0' cysteine with hydrogen on the sulfur
    • 'cs' cysteine in a disulfide bond
    • 'd-' aspartic acid deprotonated
    • 'e-' glutamic acid deprotonated
    • 'f0' phenylalanine
    • 'g0' glycine
    • 'h+' histidine both N protonated
    • 'hd' histidine neutral with only Nd protonated
    • 'he' histidine neutral with only Ne protonated
    • 'i0' isoleucine
    • 'k+' lysine protonated
    • 'l0' leucine
    • 'm0' methionine
    • 'n0' asparagine
    • 'p0' proline
    • 'q0' glutamine
    • 'r+' arginine protonated
    • 's0' serine
    • 't0' threonine
    • 'v0' valine
    • 'w0' tryptophan
    • 'y0' tyrosine
    • 'za' acetyl cap on the N-terminus
    • 'zm' amide cap (NH2) 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.
    • 'zn' N-methylamide cap on the C-terminus
Nucleic acids
    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. .
    • 'A' adenosine (AMP)
    • 'dA' deoxyadenosine (dAMP)
    • 'C' cytidine (CMP)
    • 'dC' deoxycytidine (dCMP)
    • 'G' guanosine (GUA)
    • 'dG' deoxyguanosine (dGUA)
    • 'T' thymidine (TMP)
    • 'dT' deoxythymidine (dTMP)
    • 'U' uridine (UMP)
    • 'dU' deoxyuridine (dUMP)

 

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Send comments to: Marcus G. Martin
Last updated: October 17, 2006