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MCCCS Towhee (OPLS-ua)

 

 

Overview
    This section covers the OPLS-ua force field as it is implemented into the towhee_ff_OPLS-ua file in the ForceFields directory. All of the Towhee atom types for the OPLS-ua force field are listed, along with a short description of their meanings. For more information about the OPLS family of force fields see the Jorgensen group home page. Note that OPLS-ua is a Lennard-Jones (12-6) force field and can only be combined with other Lennard-Jones (12-6) force fields. The rather famous OPLS water models are not included here as they are provided in their own force field files. Please see the TIP3P, TIP4P, and TIP5P web pages for more information about those water models. Note that OPLS-ua was followed up with an all-atom version of the force field called OPLS-aa and has been reparameterized into what I call OPLS-2001. Any discrepencies (especially typos) from the published OPLS-ua 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 OPLS-ua OPLS-ua in Towhee
    The official force field name for OPLS-ua in Towhee is 'OPLS-ua'. Here I list all of the OPLS-ua atom names for use in the towhee_input file, along with a brief description taken from the OPLS-ua literature. I have used my own judgement in creating naming conventions as they are not well defined in the literature. Please note that the capitalization and spacing pattern is important and must be followed exactly as listed here.
      Carbon (CH3 United-Atoms)
    • 'CH4' : United-atom Methane
    • 'CH3-C1' : CH3 united-atom consisting of 1 C and 3 H that is bonded to another carbon that is not in turn bonded to any other carbons(example: ethane methyl group, acetonitrile methyl group)
    • 'CH3-C2' : CH3 united-atom consisting of 1 C and 3 H that is bonded to another carbon that has 2 non-H neighbors (example: n-alkane methyl group), or is bonded to a sulfur that is in turn bonded to a hydrogen (example: thiols).
    • 'CH3-C3' : CH3 united-atom consisting of 1 C and 3 H that is bonded to another carbon that has 3 non-H neighbors (example: isobutane methyl group).
    • 'CH3-C4' : CH3 united-atom consisting of 1 C and 3 H that is bonded to another carbon that has 4 non-H neighbors (example: neopentane methyl group)
    • 'CH3-X' : CH3 united-atom consisting of 1 C and 3 H that is bonded to an atom other than carbon that is in turn bonded to another non-hydrogen atom or more than one hydrogram atom (example: sulfides, disulfides, N-methylacetamide, dimethylformamide, methyl-acetate).
    • Carbon (CH2 United-Atoms)
    • 'CH2sp3-SR' : CH2 united-atom consisting of 1 C and 2 H with an sp3 hybridization on the C that is bonded to a sulfur that is in turn bonded to another non-hydrogen atom (example: sulfides and disulfides).
    • 'CH2sp3-N' : CH2 united-atom consisting of 1 C and 2 H with an sp3 hybridization on the C that is bonded to a nitrogen (example: Calpha in glycine, C in proline).
    • 'CH2sp3' : CH2 united-atom consisting of 1 C and 2 H with an sp3 hybridization on the C.
    • 'CH2sp2' : CH2 united-atom consisting of 1 C and 2 H with an sp2 hybridization on the C.
    • Carbon (CH United-Atoms)
    • 'CHsp3-N' : CH united-atom consisting of 1 C and 1 H with an sp3 hybridization on the C that is bonded to a Nitrogen (example: Calpha in Ala, Calpha in Pro).
    • 'CHsp3' : CH united-atom consisting of 1 C and 1 H with an sp3 hybridization on the C.
    • 'CHsp2-N' : CH united-atom consisting of 1 C and 1 H with an sp2 hybridization on the C that is bonded to a Nitrogen (example: formamide).
    • 'CHsp2' : CH united-atom consisting of 1 C and 1 H with an sp2 hybridization on the C.
    • 'CHarom' : CH united-atom consisting of 1 C and 1 H with an aromatic C.
    • Carbon Atoms
    • 'Csp3' : C atom consisting of 1 C bonded to 0 H with an sp3 hybridization on the C.
    • 'Csp2' : C atom consisting of 1 C bonded to 0 H with an sp2 hybridization on the C.
    • 'Csp' : C atom consisting of 1 C bonded to 0 H with an sp hybridization on the C (example: central C in acetonitrile).
    • Chlorine
    • 'Cl-' : Cl ion with a negative 1.0 charge.
    • Fluorine
    • 'F' : F in Hydrogen Fluoride.
    • 'F-' : F ion with a negative 1.0 charge.
    • Hydrogen
    • 'H' : H atom bonded to something other than a carbon.
    • Lithium
    • 'Li+' : Li ion with a positive 1.0 charge.
    • Nitrogen
    • 'Nsp2' : Nitrogen bonded to 3 other atoms in a trigonal planar arrangement (example: amides and amino acids).
    • 'Ns' : Nitrogen triple bonded to one other atom (example: acetonitrile).
    • Oxygen
    • 'Osp3' : sp3 hybridization on an O atom that is bonded to two other atoms.
    • Sodium
    • 'Na+' : Na ion with a positive 1.0 charge.
    • Sulfur
    • 'S-HSH' : sulfur bonded to 2 hydrogen atoms.
    • 'S-RSR' : sulfur bonded to 2 atoms where at least one of those atoms is not a hydrogen.
Coulombic interactions
    OPLS-ua uses atom-centered point charges to represent the electrostatic interactions. You need to look through the OPLS-ua literature to find molecules with similar moieties to the ones on the molecule you wish to simulate. Here I list some examples.
    Alcohols (from Jorgensen 1986 alcohols)
    • 'H': -0.700
    • 'Osp3': 0.435
    • 'C' that is bonded directly to the oxygen: 0.265
    Thiols (from Jorgensen 1986 sulfur)
    • 'H': 0.27
    • 'S-RSR': -0.45
    • 'CH*' bonded to the thiol sulfur: 0.18
    Sulfides (from Jorgensen 1986 sulfur)
    • 'CH3-SR' or 'CH2sp3-SR': 0.235
    • 'S-RSR': -0.47
    • 'CH3-SR' or 'CH2sp3-SR': 0.235
    Disulfides (from Jorgensen 1986 sulfur)
    • 'CH3-SR' or 'CH2sp3-SR': 0.30
    • 'S-RSR': -0.30
    • 'S-RSR': -0.30
    • 'CH3-SR' or 'CH2sp3-SR': 0.30
    SH2 (from Jorgensen 1986 sulfur)
    • 'H': 0.235
    • 'S-HSH': -0.47
    • 'H': 0.235
    HF (from Cournoyer and Jorgensen 1984)
    • 'H': 0.64942
    • 'F': -0.64942
    Parameters for Amides and Peptides (from Jorgensen and Swenson 1985)
    • 'Nsp2' (1o) formamide, Asn: -0.85
    • 'Nsp2' (2o) NMA, Ala: -0.57
    • 'Nsp2' (3o) DMF, Pro: -0.57
    • 'H' (N1o) formamide, Asn: 0.425
    • 'H' (N2o) NMA, Ala: 0.37
    • 'Osp2' (C=O) amides: -0.50
    • 'Csp2' (C=O) NMA, Ala: 0.50
    • 'CHsp2-N' (CH=O) formamide: 0.50
    • 'CH3-N' (N2o) NMA: 0.20
    • 'CH3-N' (N3o) DMF: 0.285
    • 'CH2sp3-N' Calpha in Gly: 0.20
    • 'CHsp3-N' Calpha in Ala: 0.20
    • 'CHsp3-N' Calpha in Pro: 0.285
    • 'CH2sp3-N' Pro: 0.285
    • 'CH3-N' (C=O) NMA: 0.0
    Acetonitrile (from Jorgensen and Briggs 1988)
    • 'CH3-C1': 0.15
    • 'Csp': 0.28
    • 'Ns': -0.43
Improper torsions
    There are no improper torsions currently implemented for this force field.
Proteins
    The protein builder is not implemented for this force field.
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Send comments to: Marcus G. Martin
Last updated: September 07, 2005