Overview
This section covers an early force field in the Amber family called the Weiner et al. 1986 force field
as it is implemented into the Towhee code. All of the Towhee atom types for the Weiner et al. 1986 force
field are listed, along with a short description of their meanings.
Weiner et al. 1986 is an extension of a a previous force field called
Weiner et al. 1984 that contained a substantial subset of the atom types
available in Weiner et al. 1986, although please note that there were several small changes in parameters
between 1984 and 1986. Additional parameters for Weiner et al. 1986 were later added for pentaerythritrol
tetranitrate as decribed in the Dick and Ritchie 1994 manual.
Note that Weiner et al. 1986 is a 12-6 plus 12-10 H-bond force field and can only be combined with
other '12-6 plus 12-10 H-bond' force fields.
Any discrepencies (especially typos) from the published force field values are the sole responsibility
of Marcus Martin, and I welcome feedback on how this implementation compares with other programs.
References for Weiner et al. 1986
Weiner et al. 1986 in Towhee
The official force field name for Weiner et al. in Towhee is 'Weiner1986' and the file name is
towhee_ff_Weiner1986 in the ForceFields directory. Here I list all of
the atom names for use in the towhee_input file, along with a brief description taken
from the Weiner et al. 1984 and
Weiner et al. 1986 papers.
Please note that the capitalization and spacing pattern is important
and must be followed exactly as listed here.
- Carbon (united or atomic)
- 'C2' : united sp3 carbon with two hydrogens
- 'C3' : united sp3 carbon with three hydrogens
- 'CD' : united sp2 aromatic carbon in six-membered ring with one hydrogen
- 'CE' : united sp2 aromatic carbon in five-membered ring between two nitrogens with
one hydrogen (in purines)
- 'CF' : united sp2 aromatic carbon in five-membered ring next to a nitrogen without a
hydrogen (e.g., Cdelta-Nepsilon=Cepsilon in histidine)
- 'CG' : united sp2 aromatic carbon in five membered ring next to a N-H
(e.g., Cdelta-Nepsilon=Cepsilon in histidine)
- 'CH' : united sp3 carbon with one hydrogen
- 'CI' : united sp2 carbon in six-membered ring of purines between two "NC" nitrogens
- 'CJ' : united sp2 carbon in pyrimidines at positions 5 and 6 (more pure double bond
than aromatic) with one hydrogen
- 'CP' : united sp2 aromatic carbon in five-membered ring between two nitrogens with one hydrogen (in His)
- 'C' : atomic sp2 carbonyl carbon and aromatic carbon with hydroxyl substituent in tyrosine
- 'C*' : atomic sp2 aromatic carbon in five-membered ring with one substituent
(e.g., CEgamma in Trp)
- 'CA' : atomic sp2 aromatic carbon in six-membered ring with one substituent
- 'CB' : atomic sp2 aromatic carbon at junction between five- and six-membered rings (e.g., CEdelta
in Trp, C4 and C5 in purines)
- 'CC' : atomic sp2 aromatic carbon in five-membered ring with one substituent and next to a nitrogen group
(e.g., Cgamma in His)
- 'CK' : atomic sp2 aromatic carbon in five-membered ring between two nitrogens and bonded to one hydrogen (in purines)
- 'CM' : atomic sp2 same as CJ but one substituent
- 'CN' : atomic sp2 aromatic junction carbon in between five- and six-membered rings (e.g., Cepsilon
in Trp)
- 'CQ' : atomic sp2 carbon in six membered ring of purines between two "NC" nitrogens and bonded to one hydrogen.
- 'CR' : atomic sp2 aromatic carbon in five membered ring between two nitrogens and bonded to one hydrogen (in HIS)
- 'CT' : atomic sp3 carbon with four explicit substituents
- 'CV' : atomic sp2 aromatic carbon in five membered ring bonded to an N: and bonded to an explicit hydrogen
(e.g. Cdelta-Nepsilon=Cepsilon in HIS)
- 'CW' : atomic sp2 aromatic carbon in five membered ring bonded to an N-H and bonded to an explicit hydrogen
(e.g. Cdelta-Nepsilon-Cepsilon in HIS).
- Hydrogen (all atomic)
- 'H3' : hydrogens of lysine and arginine (positively charged)
- 'H2' : amino hydrogens from NH2 in purines and pyrimidines
- 'HC' : explicit hydrogen attached to carbon
- 'H' : amide and imino hydrogens
- 'HO' : hydrogen on hydroxyl or water oxygen
- 'HS' : hydrogen attached to sulfur
- Nitrogen (all atomic)
- 'NC' : sp2 nitrogen in six-membered ring with lone pairs (e.g., N3 in adenine)
- 'NA' : sp2 nitrogen in five-membered ring with hydrogen attached (e.g., protonated His)
- 'NB' : sp2 nitrogen in five-membered ring with lone pairs (e.g., N7 in purines)
- 'N*' : sp2 nitrogen in purines and pyrimidines with alkyl group attached
(N9 in purines. N1 in pyrimidines)
- 'N' : sp2 nitrogen in amide groups
- 'N2' : sp2 nitrogen in base NH2 groups and arginines NH2
- 'N3' : sp3 nitrogen with four substituents (e.g., Lys Nzeta
- 'NT' : sp3 nitrogen with three substituents (e.g., unprotonated amines)
- Oxygen (all atomic)
- 'O' : carbonyl oxygen
- 'O2' : corboxyl and phosphate nonbonded oxygens
- 'OS' : ether and ester oxygens
- 'OH' : alcohol oxygens
- Phosphorus (all atomic)
- 'P' : phosphorus in phosphate groups
- Sulfur (all atomic)
- 'S' : sulfurs in disulfide linkages and mentioning
- 'SH' : sulfur in cycstine
- 'LP' : lone pairs attached to sulfur
Coulombic Interactions
Weiner et al. 1986 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.
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. Weiner et al. 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. However, they are
also centered on some united-atoms in order to enforce stereochemistry. 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.
Please see the Weiner et al. 1986 paper for more
information about assigning improper torsions for this force field.
Proteins
This force field contains parameters for all of the amino acids, but these have not yet been implemented into the
polymer builder in Towhee. If anyone is interested in implementing this functionality for this force field please
contact the Towhee developers.
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