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MCCCS Towhee (Amber param96)

 

 

Overview
    This section covers the Amber param96 force field as it is implemented into the Towhee code. All of the Towhee atom types for the Amber param96 force field are listed, along with a short description of their meanings. For more information about the Amber force field see the Amber web site. Note that Amber param96 is a Lennard-Jones (12-6) force field and can only be combined with other Lennard-Jones (12-6) force fields. I would like to acknowledge Wendy D. Cornell and the late Peter A. Kollman for providing very useful guidance about implementing Amber param96. Any discrepencies (especially typos) from the published Amber param96 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 Amber param96 Amber param96 in Towhee
    The official force field name for Amber param96 in Towhee is 'Amber96' and the file name is towhee_ff_Amber96 in the ForceFields directory. Here I list all of the Amber96 atom names for use in the towhee_input file, along with a brief description taken from the Cornell et al. paper. I have added some comments where I thought clarification was needed, these are all in [square brackets]. Please note that the capitalization and spacing pattern is important and must be followed exactly as listed here.
      Carbon
    • 'CT' : any sp3 carbon
    • 'C' : any carbonyl sp2 carbon
    • 'CA' : any aromatic sp2 carbon and (Cepsilon of Arg)
    • 'CM' : any sp2 carbon, double bonded
    • 'CC' : sp2 aromatic in 5-membered ring with one substituent + next to nitrogen (Cgamma in His)
    • 'CV' : sp2 aromatic in 5-membered ring next to carbon and lone pair nitrogen (e.g. Cdelta in His(delta))
    • 'CW' : sp2 aromatic in 5-membered ring next to carbon and NH (e.g. Cdelta in His(epsilon) and in Trp)
    • 'CR' : sp2 aromatic in 5-membered ring next to two nitrogens (Cgamma and Cepsilon in His)
    • 'CB' : sp2 aromatic at junction of 5- and 6-membered rings (Cdelta in Trp) and both junction atoms in Ade and Gua
    • 'C*' : sp2 aromatic in 5-membered ring next to two carbons (e.g. Cgamma in Trp)
    • 'CN' : sp2 junction between 5- and 6-membered rings and bonded to CH and NH (Cepsilon in Trp)
    • 'CK' : sp2 carbon in 5-membered aromatic between N and N-R (C8 in purines)
    • 'CQ' : sp2 carbon in 6-membered ring between lone pair nitrogens (e.g. C2 in purines)
    • Chlorine
    • 'Cl-' : ionic chlorine (-1 charge)
    • Hydrogen
    • 'H' : H attached to N
    • 'HA' : H attached to aromatic carbon with no electronegative neighbors
    • 'HC' : H attached to aliphatic carbon with no electron-withdrawing substituents
    • 'H1' : H attached to aliphatic carbon with one electron-withdrawing substituent
    • 'H2' : H attached to aliphatic carbon with two electron-withdrawing substituents
    • 'H3' : H attached to aliphatic carbon with three electron-withdrawing substituents
    • 'HW' : H in TIP3P water
    • 'HO' : H in alcohols and acids
    • 'HS' : H attached to sulfur
    • 'HP' : H attached to carbon directly bonded to formally positive atoms (e.g C next to NH3+ of lysine)
    • 'H4' : H attached to aromatic carbon with one electronegative neighbor (e.g hydrogen on C5 of Trp, C6 of Thy)
    • 'H5' : H attached to aromatic carbon with two electronegative neighbors (e.g H8 of Ade and Gua and H2 of Ade)
    • Nitrogen
    • 'N' : sp2 nitrogen in amides
    • 'NA' : sp2 nitrogen in aromatic rings with hydrogen attached (e.g. protonated His, Gua, Trp)
    • 'NB' : sp2 nitrogen in 5-membered ring with lone pair (e.g. N7 in purines)
    • 'NC' : sp2 nitrogen in 6-membered ring with lone pair (e.g. N3 in purines)
    • 'N*' : sp2 nitrogen in 5-membered ring with carbon substituent (in purine nucleosides)
    • 'N2' : sp2 nitrogen of aromatic amines and guanidinium ions
    • 'N3' : sp3 nitrogen
    • Oxygen
    • 'OW' : sp3 oxygen in TIP3P water
    • 'OH' : sp3 oxygen in alcohols, tyrosine, and protonated carboxylic acids
    • 'OS' : sp3 oxygen in ethers
    • 'O' : sp2 oxygen in amides
    • 'O2' : sp2 oxygen in anionic acids
    • Phosphorous
    • 'P' : phosphorus in phosphates
    • Sulfur
    • 'S' : sulfur in methionine and cysteine [sulfide form of cysteine]
    • 'SH' : sulfur in cysteine [thiol form of cysteine]
Coulombic Interactions
    Amber 96 uses point charges located at atomic centers to represent the elecrostatic interactions between atoms. There is no simple, general table of charges for atoms in this force field. Instead, they recommend using the RESP method to fit the charges for each molecule of interest. See the Amber web site for more information about this method. See the protein section below for comments on the Amber param96 charges used with the protein builder.
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. Amber param96 exclusively uses the Stereocenter version of the improper torsions, and they are typically centered on an sp2 atom in order to enforce planarity with its three neighbors. Only one improper torsion allowed to be centered on any atom. These torsions are listed in the Amber literature as i-j-k-l where the angle is the dihedral between i-k-l and j-k-l, and the bonding pattern is i, j, and l are all bonded to atom k, and are also not bonded to each other. In the towhee_input file this stereo improper torsion is listed only for atom k, and the atom order there is l, i, j. 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 Amber96 force field. I have implemented the atom types and charges according to the published Amber param96 values except in the following cases.
    • N-terminal leucine: the electronic files for Amber param96 list CD1 with a charge of -0.41060 and atom CD2 with a charge of -0.41040. These atoms are symmetric and indistinguishable in reality so I felt it made no sense to give them different charges just because they have different names. Therefore I put a charge of -0.41050 on both atoms.
    • N-terminal phenylalanine: the electronic files for Amber param96 list CE1 with a charge of -0.16020 and atom CE2 with a charge of -0.16030. These atoms are symmetric and indistinguishable in reality so I put a charge of -0.16025 on both atoms.
    Here is a complete list of the groups for Amber96.
    • 'a0' alanine
    • 'c0' cysteine with hydrogen on the sulfur
    • 'cs' cysteine in a disulfide bond
    • 'cp' cysteine bonded to palmitate (includes the palmitate)
    • '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
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Send comments to: Marcus G. Martin
Last updated: May 12, 2006