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MCCCS Towhee (OPLS-aa)

 

 

Overview
    This section covers the OPLS-aa force field as it is implemented into the towhee_ff_OPLS-aa file in the ForceFields directory. All of the Towhee atom types for the OPLS-aa force field are listed, along with a short description of their meanings. For more information about the OPLS-aa force field see the Jorgensen group home page. Note that OPLS-aa 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-aa was preceded by a united-atom version of the force field called OPLS-ua and has been reparameterized into what I call OPLS-2001. I would like to acknowledge W.L. Jorgensen for kindly providing me with an electronic copy of the OPLS-aa parameters. Any discrepencies (especially typos) from the published OPLS-aa 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-aa OPLS-aa in Towhee
    The official force field name for OPLS-aa in Towhee is 'OPLS-aa'. Here I list all of the OPLS-aa atom names for use in the towhee_input file, along with a brief description taken from the OPLS-aa literature. Notice that OPLS-aa uses almost the same naming conventions as the Amber param96 force field. This is not a coincedence as these force fields utilize many of the same bonded interaction terms. I have modified some of the atom names from the standard OPLS-aa in order to create unique type names. This was needed because OPLS-aa occasionally uses different bonded interactions for atoms which have the same atom name for nonbonded interactions. I do not always distinguish between the original OPLS-aa comments, and my modifications as I have created several new atom names. Some of my comments are placed in [square brackets]. Please note that the capitalization and spacing pattern is important and must be followed exactly as listed here.
      Bromine
    • 'Br-' : bromine ion (charge -1)[uses the parameters from the LGM force field]
    • Carbon
    • 'C a' : carbon in O-C=O acid
    • 'C k' : carbon in C=O not bonded to N, and not an acid group
    • 'C n' : carbon in N-C=O
    • 'C*' : aromatic C in 5-membered ring next to two carbons
    • 'CA~' : neutral aromatic carbon not at the junction of 5-membered and 6-membered rings
    • 'CA+' : aromatic carbon in guanidinium C+
    • 'CAj' : neutral aromatic carbon at the juction of 5-membered and 6-membered rings
    • 'CAxna' : special parameters for nucleotide bases. aromatic C in DAP C2,C3,C4 pyridine; Cytosine C4,C5,C6
    • 'CBxna' : special parameters for nucleotide bases. Adenine C4,C5,C6; Guanine C2,C4,C5
    • 'CB' : aromatic C at juntion of 5-membered and 6-membered rings
    • 'CKxna' : special parameters for nucleotide bases. Adenine C8 Guanine
    • 'CM' : alkene sp2 carbon (non-aromatic)
    • 'CMxna' : special parameters for nucleotide bases. Carbon in Uracil C5,C6
    • 'CN' : aromatic carbon in tryptophan at position CE2.
    • 'CO' : sp3 anomeric carbon (bonded to ether O and alcohol O). this type shows up in carbohydrates
    • 'CQ' : sp2C in 6-membered ring between deprotonated N's
    • 'CR' : aromatic C in 5-membered ring next to two nitrogens
    • 'CS' : aromatic C which does not have 120 degree bond angles with all of its neighbors. Examples are C3 in pyrrole and C3 in furan
    • 'CT' : aliphatic sp3 hybrid carbon
    • 'CTf' : aliphatic sp3 hybrid carbon bonded to F
    • 'CTxna' : special parameters for nucleotide bases. Thymine C-C5, 9-Me A or G C-N9
    • 'CU' : aromatic C which abuts NB in a heteroatom-heteroatom bond. Examples are C3 in pyrazole and C3 in isoxazole
    • 'CV' : aromatic C in 5-membered ring next to C and deprotonated N
    • 'CW' : sp2 aromatic C in 5-membered ring next to C and NH
    • Chlorine
    • 'Cl' : chlorine bonded to a carbon
    • 'Cl-' : chlorine ion (charge -1)
    • Fluorine
    • 'F' : fluorine nonionic
    • 'F-' : fluorine ion (charge -1)
    • Hydrogen
    • 'H' : H attached to N
    • 'H2xna' : special parameters for nucleotide bases. DAP H-amine, Cytosine, Adenine
    • 'HA' : H bonded to an aromatic ring
    • 'HC~1' : hydrogen attached to an sp3 carbon in most cases, see special cases of hydrogen below
    • 'HC~2' : H bonded to a non-aromatic sp2 carbon which is not bonded to a N, not double bonded to O, and is not bonded to C=O
    • 'HC~3' : H bonded to a C=O or bonded to a C which is bonded to a C=O
    • 'HC~4' : H bonded to a CT that is bonded to NT
    • 'HCxna' : special parameters for nucleotide bases. DAP H3,H4; Uracil H-C5,H-C6; Thymine H-CC5; Cytosine H-C5,H-C6; Adenine H-C2,H-C8; Guanine
    • 'HO' : H attached to O in alcohol
    • 'HS' : H attached to S
    • Iodine
    • 'I-' : iodine ion (charge -1)
    • Lithium
    • 'Li+' : lithium ion (charge +1)
    • Nitrogen
    • 'N' : N in an amide
    • 'N2' : sp2 N of aromatic amines and guanidinium ions
    • 'N3~' : sp3 neutral N of amines. NOTE: the N3 parameters are obsoleted by the NT parameters. I have included them here in case you want to study these older parameters, but I would recomend using the NT versions.
    • 'N3+' : sp3 N ammonium ions (charge +1). NOTE: the N3 parameters are obsoleted by NT parameters. I have included them here in case you want to study these older parameters, but I would recomend using the NT versions.
    • 'NA' : sp2 aromatic N with H attached
    • 'NB' : sp2 N in 5-membered ring, deprotonated
    • 'NC' : sp2 N in 6-membered ring, deprotonated
    • 'NO' : sp2 N in a nitro group
    • 'NT~1' : sp3 N in ammonia
    • 'NT+1' : sp3 N in ammonium ion (charge +1)
    • 'NT~2' : sp3 N in primary, secondary, tertiary amine
    • 'NT+2' : sp3 N in primary, secondary, tertiary ammonium ion (charge +1)
    • Oxygen
    • 'O' : oxygen in C=O, not an acidic site
    • 'O2' : oxygen double bonded to carbon in COO- or COOH
    • 'OHa' : oxygen bonded to H in RCOOH
    • 'OHm' : oxygen bonded to H in a mono-alcohol
    • 'OHp' : oxygen bonded to H in polyols or phenol
    • 'OS' : sp3 O in an ether or acetal
    • Sodium
    • 'Na+' : sodium ion (charge +1)
    • Sulfur
    • 'S' : S in sulfide, disulfide
    • 'SH' : S in thiols
Coulombic interactions
    OPLS-aa uses atom-centered point charges to represent the electrostatic interactions. I do not know of an automated way to assign these point charges. Instead, you need to look through the OPLS-aa literature to find molecules with similar moieties to the ones on the molecule you wish to simulate.
Improper torsions
    OPLS-aa uses stereocenter improper torsions to enforce planarity in aromatic rings, around amide nitrogens, and around other sp2 carbons. 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). Improper torsions for proteins are exactly the same as implemented in AMBER96 - even though OPLS puts the stereocenter in the second position of the torsion, you still define them in towhee putting it in the first position (towhee automatically adjusts the parameter order for you).
Proteins
    The OPLS-aa protein builder has been implemented with all charges verbatim from WLJ 1996. (Note that the sidechain charges on Met and Cys were later revised in OPLS-2001). Because many of the bonded parameters are unpublished, they have been cobbled together from other OPLS-aa implementations, namely ffoplsaabon.itp in GROMACS 3.2.1 and oplsaa.prm in TINKER 4.0- the origin of added parameters is referenced in the comments of ffoplsaa.F. Most of the missing parameters merely required additional aliases to existing entries because of the above naming convention. Note that GROMACS uses nanometers and KJoules instead of Angstroms and Kcals so unit conversions are necessary when comparing Towhee and GROMACS results. Here 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. Despite a great deal of effort this amino acid is still not working properly with this forcefield as there are many parameters that are missing. You will get an error if you include this amino acid for this forcefield.
    • 'y0' tyrosine
    • 'za' acetyl cap on the N-terminus
    • 'zm' amide cap (NH2) on the C-terminus.
    • 'zn' N-methylamide cap on the C-terminus
    • 'zf' formaldahyde cap on the N-terminus
Return to the Towhee Capabilities web page

 


Send comments to: Marcus G. Martin
Last updated: June 28, 2006