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MCCCS Towhee (MMFF94)

 

 

Overview
    This section covers the MMFF94 force field as it is implemented into the towhee_ff_MMFF94 file in the ForceFields directory. This force field was parameterized for a wide variety of organic liquids. Note that this is a Class-2 'Buffered 14-7' force field that uses the 'MMFF' mixing rules. Any discrepencies (especially typos) from the published values are the sole responsibility of Marcus G. Martin, and I welcome feedback on how this implementation compares with other programs.
References for MMFF94 Typos and comments for MMFF94
  • The supplementary information is very useful and is available via anonymous ftp at ftp.wiley.com in the /public/journals/jcc/suppmat/17/490 directory. Those files are the primary source for the implementation in Towhee.
  • A useful test suite of compounds and MMFF energies is available at http://www.ccl.net/cca/data/MMFF94/. The Towhee implementation was validated for a handful of these compounds startimg with version 7.2.0 and this led to the discovery (and resolution) of many mistakes that existed in previous implementations. This implmentation is still not fully validated for the entire test suite so testing is highly recomended before using this forcefield.
MMFF94 in Towhee
    The official force field name for MMFF94 in Towhee is 'MMFF94'. This section provides a complete list of the implemented nonbonded parameter names for use in the towhee_input file, along with a brief description. The names and descriptions are taken from the MMFFSYMB.PAR section of appendix B in the supplementary information file. The (MMFF number) included in the description is the integer code used in the internals of the MMFF force field. If two atom types have the same number then they have the same interactions. That means there are redundant atom types in the MMFF force field. These names and descriptions are from Table III of Halgren 1996 (I). A note is added when the base charge of the atom (before applying the bond increment method of charge assignement) is nonzero. Note that the capitalization and spacing pattern is important and must be followed exactly as listed here.
      Bromine
    • BR : (MMFF number 13) BROMINE
    • BR- : (MMFF number 91) BROMIDE ANION
    • Calcium
    • CA+2 : (MMFF number 96) DIPOSITIVE CALCIUM
    • Carbon
    • CR : (MMFF number 1) ALKYL CARBON, SP3
    • C=C : (MMFF number 2) VINYLIC CARBON, SP2
    • CSP2 : (MMFF number 2) GENERIC SP2 CARBON
    • C=O : (MMFF number 3) GENERAL CARBONYL CARBON
    • C=N : (MMFF number 3) SP2 CARBON IN C=N
    • CGD : (MMFF number 3) GUANIDINE CARBON, DOUBLY BONDED TO N
    • C=OR : (MMFF number 3) KETONE OR ALDEHYDE CARBONYL CARBON
    • C=ON : (MMFF number 3) AMIDE CARBONYL CARBON
    • CONN : (MMFF number 3) UREA CARBONYL CARBON
    • COO : (MMFF number 3) CARBOXYLIC ACID OR ESTER CARBONYL CARBON
    • COON : (MMFF number 3) CARBAMATE CARBONYL CARBON
    • COOO : (MMFF number 3) C ARBONIC ACID OR ESTER CARBONYL CARBON
    • C=OS : (MMFF number 3) THIOESTER CARBONYL CARBON, DOUBLE BONDED TO O
    • C=S : (MMFF number 3) THIOESTER CARBON, DOUBLY BONDED TO S
    • C=SN : (MMFF number 3) THIOAMIDE, CARBON, DOUBLY BONDED TO S
    • CSO2 : (MMFF number 3) CARBON IN >C=SO2
    • CS=O : (MMFF number 3) CARBON IN >C=S=O (SULFINYL GROUP)
    • CSS : (MMFF number 3) THIOCARBOXYLIC ACID OR ESTER CARBONYL CARBON
    • C=P : (MMFF number 3) CARBON DOUBLE BONDED TO PHOSPHOROUS
    • CSP : (MMFF number 4) ACETYLENIC CARBON
    • =C= : (MMFF number 4) ALLENIC CARBON
    • CR4R : (MMFF number 20) CARBON IN 4-MEMBERED RINGS
    • CR3R : (MMFF number 22) CARBON IN A 3-MEMBERED RING
    • CE4R : (MMFF number 30) OLEFINIC CARBON IN 4-MEMBERED RINGS
    • CB : (MMFF number 37) CARBON AS IN BENZENE, PYRROLE
    • CO2M : (MMFF number 41) CARBOXYLATE ANION CARBON (base charge -0.5)
    • CS2M : (MMFF number 41) CARBON IN THIOCARBOXYLATE ANION
    • CGD+ : (MMFF number 57) GUANIDINIUM CARBON
    • CNN+ : (MMFF number 57) C IN +N=C-N RESONANCE STRUCTURES
    • C% : (MMFF number 60) ISONITRILE CARBON
    • C5A : (MMFF number 63) ALPHA CARBON IN 5-MEMBERED HETEROAROMATIC RING
    • C5B : (MMFF number 64) BETA CARBON IN 5-MEMBERED HETEROAROMATIC RING
    • C5 : (MMFF number 78) GENERAL CARBON IN 5-MEMBERED HETEROAROMATIC RING
    • CIM+ : (MMFF number 80) C IN N-C-N IN IMIDAZOLIUM ION
    • Chlorine
    • CL : (MMFF number 12) CHLORINE
    • CLO4 : (MMFF number 77) CHLORINE IN PERCHLORATE ANION, CLO4(-)
    • CL- : (MMFF number 90) CHLORIDE ANION
    • Copper
    • CU+1 : (MMFF number 97) MONOPOSITIVE COPPER
    • CU+2 : (MMFF number 98) DIPOSITIVE COPPER
    • Fluorine
    • F : (MMFF number 11) FLUORINE
    • F- : (MMFF number 89) FLUORIDE ANION
    • Hydrogen
    • HC : (MMFF number 5) H ATTACHED TO C
    • HSI : (MMFF number 5) H ATTACHED TO SI
    • HOR : (MMFF number 21) HYDROGEN IN ALCOHOLS
    • HO : (MMFF number 21) GENERAL H ON OXYGEN
    • HOM : (MMFF number 21) HYDROGEN IN HYDROXIDE ANION
    • HNR : (MMFF number 23) H-N(SP3)
    • H3N : (MMFF number 23) H-N(SP3), AMMONIA
    • HPYL : (MMFF number 23) H-N IN PYRROLE
    • HNOX : (MMFF number 23) H-N IN IN A N-OXIDE
    • HNM : (MMFF number 23) H ON DICOORD, NEGATIVELY CHARGED NITROGEN
    • HN : (MMFF number 23) GENERAL H ON NITROGEN
    • HOCO : (MMFF number 24) H-O IN CARBOXYLIC ACIDS
    • HOP : (MMFF number 24) HYDROGEN ON OXYGEN ATTACHED TO PHOSPHOROUS
    • HN=N : (MMFF number 27) AZO HYDROGEN
    • HN=C : (MMFF number 27) IMINE HYDROGEN
    • HNCO : (MMFF number 28) AMIDE HYDROGEN
    • HNCS : (MMFF number 28) THIOAMIDE HYDROGEN
    • HNCC : (MMFF number 28) H-N IN ENAMINES
    • HNCN : (MMFF number 28) H-N IN H-N-C=N
    • HNNC : (MMFF number 28) H-N IN H-N-N=C
    • HNNN : (MMFF number 28) H-N IN H-N-N=N
    • HNSO : (MMFF number 28) H-N IN SULFONAMIDE
    • HNPO : (MMFF number 28) H-N IN PHOSPHONAMIDE
    • HNC% : (MMFF number 28) HYDROGEN ON N ATTACHED TO TRIPLY BONDED CARBON
    • HSP2 : (MMFF number 28) GENERAL H ON SP2 NITROGEN
    • HOCC : (MMFF number 29) H-O IN ENOLS AND PHENOLS
    • HOCN : (MMFF number 29) H-O IN HO-C=N
    • HOH : (MMFF number 31) HYDROGEN IN H2O
    • HOS : (MMFF number 33) H ON OXYGEN ATTACHED TO SULFUR
    • HNR+ : (MMFF number 36) H ON QUATERNARY NITROGEN
    • HIM+ : (MMFF number 36) H ON IMIDAZOLIUM-TYPE NITROGEN
    • HPD+ : (MMFF number 36) H ON PROTONATED PYRIDINE NITROGEN
    • HNN+ : (MMFF number 36) H ON AMIDINIUM-TYPE NITROGEN
    • HNC+ : (MMFF number 36) H ON PROTONATED IMINE NITROGEN
    • HGD+ : (MMFF number 36) H ON GUANIDINIUM-TYPE NITROGEN
    • HN5+ : (MMFF number 36) H ON N5+, N5A+ OR N5B+
    • HO+ : (MMFF number 50) HYDROGEN ON O+ OXYGEN
    • HO=+ : (MMFF number 52) HYDROGEN ON OXENIUM OXYGEN
    • HS : (MMFF number 71) H ATTACHED TO DIVALENT, DICOORDINATE S
    • HS=N : (MMFF number 71) H ATTACHED TO TETRAVALENT, TRICOODR S DBL BONDED
    • HP : (MMFF number 71) H ATTACHED TO TRI- OR TETRACOORDINATE PHOSPHORUS
    • Iodine
    • I : (MMFF number 14) IODINE
    • Iron
    • FE+2 : (MMFF number 87) IRON +2 CATION
    • FE+3 : (MMFF number 88) IROM +3 CATION
    • Lithium
    • LI+ : (MMFF number 92) LITHIUM CATION
    • Magnesium
    • MG+2 : (MMFF number 99) DIPOSITIVE MAGNESIUM CATION
    • Nitrogen
    • NR : (MMFF number 8) NITROGEN IN ALIPHATIC AMINES
    • N=C : (MMFF number 9) NITROGEN IN IMINES
    • N=N : (MMFF number 9) NITROGEN IN AZO COMPOUNDS
    • NC=O : (MMFF number 10) NITROGEN IN AMIDES
    • NC=S : (MMFF number 10) NITROGEN IN N-C=S, THIOAMIDE
    • NN=C : (MMFF number 10) NITROGEN IN N-N=C
    • NN=N : (MMFF number 10) NITROGEN IN N-N=N
    • NR+ : (MMFF number 34) QUATERNARY NITROGEN, SP3, POSITIVELY CHARGED
    • NPYD : (MMFF number 38) NITROGEN, AS IN PYRIDINE
    • NPYL : (MMFF number 39) NITROGEN, AS IN PYRROLE
    • NC=C : (MMFF number 40) NITROGEN ON N-C=C
    • NC=N : (MMFF number 40) NITROGEN IN N-C=N
    • NC=P : (MMFF number 40) NITROGEN IN N-C=P
    • NC%C : (MMFF number 40) NITROGEN ATTACHED TO C-C TRIPLE BOND
    • NSP : (MMFF number 42) NITROGEN, TRIPLE BONDED
    • NSO2 : (MMFF number 43) NITROGEN IN SULFONAMIDES
    • NSO3 : (MMFF number 43) NITROGEN IN SULFONAMIDES, THREE O'S ON S
    • NPO2 : (MMFF number 43) NITROGEN IN PHOSPHONAMIDES
    • NPO3 : (MMFF number 43) NITROGEN IN PHOSPHONAMIDES, THREE O'S ON P
    • NC%N : (MMFF number 43) NITROGEN ATTACHED TO CYANO GROUP
    • NO2 : (MMFF number 45) NITRO GROUP NITROGEN
    • NO3 : (MMFF number 45) NITRATE GROUP NITROGEN
    • N=O : (MMFF number 46) NITROSO NITROGEN
    • NAZT : (MMFF number 47) TERMINAL NITROGEN IN AZIDO OR DIAZO GROUP
    • NSO : (MMFF number 48) DIVALENT NITROGEN REPLACING MONOVALENT O IN SO2 G
    • =N= : (MMFF number 53) NITROGEN IN C=N=N OR -N=N=N
    • N+=C : (MMFF number 54) POSITIVELY CHARGED IMINIUM NITROGEN
    • N+=N : (MMFF number 54) POSITIVELY CHARGED NITROGEN DOUBLE-BONDED TO N
    • NCN+ : (MMFF number 55) N IN +N=C-N RESONANCE STRUCTURES - FORMAL CHARGE=1/2
    • NGD+ : (MMFF number 56) GUANIDINIUM-TYPE NITROGEN - FORMAL CHARGE=1/3
    • NPD+ : (MMFF number 58) PYRIDINIUM-TYPE NITROGEN - FORMAL CHARGE=1
    • NR% : (MMFF number 61) ISONITRILE NITROGEN [FC = 0] OR DIAZO NITROGEN [F
    • NM : (MMFF number 62) DEPROTONATED SULFONAMIDE N-; FORMAL CHARGE=-1
    • N5A : (MMFF number 65) ALPHA AROM HETEROCYCLIC 5-RING NITROGEN
    • N5B : (MMFF number 66) BETA AROM HETEROCYCLIC 5-RING NITROGEN
    • N2OX : (MMFF number 67) SP2-HYDRIDIZED N-OXIDE NITROGEN
    • N3OX : (MMFF number 68) SP3-HYDRIDIZED N-OXIDE NITROGEN
    • NPOX : (MMFF number 69) PYRIDINE N-OXIDE NITROGEN
    • N5M : (MMFF number 76) NEGATIVELY CHARGED N IN, E.G, TRI- OR TETRAZOLE A
    • N5 : (MMFF number 79) GENERAL NITROGEN IN 5-MEMBERED HETEROCYCLIC RING
    • NIM+ : (MMFF number 81) IMIDAZOLIUM-TYPE NITROGEN - FORMAL CHARGE=1/2
    • N5A+ : (MMFF number 81) POSITIVE N5A NITROGEN - FORMAL CHARGE=1
    • N5B+ : (MMFF number 81) POSITIVE N5B NITROGEN - FORMAL CHARGE=1
    • N5+ : (MMFF number 81) POSITIVE N5 NITROGEN - FORMAL CHARGE=1
    • N5AX : (MMFF number 82) N-OXIDE NITROGEN IN 5-RING ALPHA POSITION
    • N5BX : (MMFF number 82) N-OXIDE NITROGEN IN 5-RING BETA POSITION
    • N5OX : (MMFF number 82) N-OXIDE NITROGEN IN GENERAL 5-RING POSITION
    • Oxygen
    • OR : (MMFF number 6) ALCOHOL OR ETHER OXYGEN
    • OC=O : (MMFF number 6) ESTER OR CARBOXYLIC ACID -O-
    • OC=C : (MMFF number 6) ENOLIC OR PHENOLIC OXYGEN
    • OC=N : (MMFF number 6) DIVALENT OXYGEN
    • OC=S : (MMFF number 6) THIOESTER OR THIOACID -O-
    • ONO2 : (MMFF number 6) DIVALENT NITRATE "ETHER" OXYGEN
    • ON=O : (MMFF number 6) DIVALENT NITRITE "ETHER" OXYGEN
    • OSO3 : (MMFF number 6) DIVALENT OXYGEN ATTACHED TO SULFUR
    • OSO2 : (MMFF number 6) DIVALENT OXYGEN ATTACHED TO SULFUR
    • OSO : (MMFF number 6) DIVALENT OXYGEN ATTACHED TO SULFUR
    • OS=O : (MMFF number 6) DIVALENT OXYGEN ATTACHED TO SULFOXIDE SULFUR
    • -OS : (MMFF number 6) GENERAL DIVALENT OX ATTACHED TO S
    • OPO3 : (MMFF number 6) DIVALENT OXYGEN ATTACHED TO PHOSPHOROUS
    • OPO2 : (MMFF number 6) DIVALENT OXYGEN ATTACHED TO PHOSPHOROUS
    • OPO : (MMFF number 6) DIVALENT OXYGEN ATTACHED TO PHOSPHOROUS
    • -OP : (MMFF number 6) DIVALENT OXYGEN ATTACHED TO PHOSPHOROUS
    • -O- : (MMFF number 6) GENERAL DIVALENT O
    • O=C : (MMFF number 7) GENERAL C=O
    • O=CN : (MMFF number 7) CARBONYL OXYGEN, AMIDES
    • O=CR : (MMFF number 7) CARBONYL OXYGEN, ALDEHYDES AND KETONES
    • O=CO : (MMFF number 7) CARBONYL OXYGEN, CARBOXYLIC ACIDS AND ESTERS
    • O=N : (MMFF number 7) NITROSO OXYGEN
    • O=S : (MMFF number 7) O=S IN SULFOXIDES
    • O=S= : (MMFF number 7) O=S ON SULFUR DOUBLY BONDED TO, E.G., CARBON
    • O2CM : (MMFF number 32) OXYGEN IN CARBOXYLATE ANION (base charge -0.25)
    • OXN : (MMFF number 32) N-OXIDE OXYGEN
    • O2N : (MMFF number 32) NITRO OXYGEN
    • O2NO : (MMFF number 32) NITRO-GROUP OXYGEN IN NITRATE
    • O3N : (MMFF number 32) NITRATE ANION OXYGEN
    • O-S : (MMFF number 32) SINGLE TERMINAL OXYGEN ON TETRACOORD SULFUR
    • O2S : (MMFF number 32) TERMINAL O-S IN SULFONES AND SULFONAMIDES
    • O3S : (MMFF number 32) TERMINAL O IN SULFONATES
    • O4S : (MMFF number 32) TERMINAL O IN SO4(-3)
    • OSMS : (MMFF number 32) TERM O IN THIOSULFINATE ANION - FORMAL CHARGE=-0.
    • OP : (MMFF number 32) TERMINAL O IN PHOSPHOXIDES
    • O2P : (MMFF number 32) TERMINAL O IN PHOSPHINATES
    • O3P : (MMFF number 32) TERMINAL OXYGEN IN PHOSPHONATES
    • O4P : (MMFF number 32) TERMINAL OXYGEN IN PHOSPHATES AND PHOSPHODIESTERS
    • O4CL : (MMFF number 32) OXYGEN IN CLO4(-) ANION - FORMAL CHARGE=-0.25
    • OM : (MMFF number 35) ALKOXIDE OXYGEN, NEGATIVELY CHARGED
    • OM2 : (MMFF number 35) OXIDE OXYGEN ON SP2 CARBON, NEGATIVELY CHARGED
    • O+ : (MMFF number 49) POSITIVELY CHARGED OXONIUM (TRICOORDINATE) OXYGEN
    • O=+ : (MMFF number 51) POSITIVELY CHARGED OXENIUM (DICOORDINATE) OXYGEN
    • OFUR : (MMFF number 59) AROMATIC OXYGEN AS IN FURAN
    • OH2 : (MMFF number 70) OXYGEN ON WATER
    • Phosphorus
    • PO4 : (MMFF number 25) PHOSPHOROUS IN PHOSPHATES AND PHOSPHODIESTERS
    • PO3 : (MMFF number 25) TETRACOORDINATE P WITH THREE ATTACHED OXYGENS
    • PO2 : (MMFF number 25) TETRACOORDINATE P WITH TWO ATTACHED OXYGENS
    • PO : (MMFF number 25) TETRACOORDINATE P WITH ONE ATTACHED OXYGEN
    • PTET : (MMFF number 25) GENERAL TETRACOORDINATE PHOSPHORUS
    • P : (MMFF number 26) TRICOORDINATE P, AS IN PHOSPHINES
    • -P=C : (MMFF number 75) PHOSPHOROUS DOUBLY BONDED TO CARBON
    • Potassium
    • K+ : (MMFF number 94) POTASSIUM CATION
    • Silicon
    • SI : (MMFF number 19) SILICON
    • Sodium
    • NA+ : (MMFF number 93) SODIUM CATION
    • Sulfur
    • S : (MMFF number 15) SULFUR IN THIOETHERS AND MERCAPTANS
    • S=C : (MMFF number 16) TERMINAL SULFUR DOUBLY BONDED TO CARBON
    • S=O : (MMFF number 17) SULFUR IN SULFOXIDES
    • >S=N : (MMFF number 17) SULFUR, TRICOORD, DOUBLY BONDED TO N
    • SO2 : (MMFF number 18) SULFUR IN SULFONES
    • SO2N : (MMFF number 18) SULFUR IN SULFONAMIDES
    • SO3 : (MMFF number 18) SULFONATE SULFUR
    • SO4 : (MMFF number 18) SULFATE SULFUR
    • =SO2 : (MMFF number 18) SULFONE SULPHER DOUBLY BONDED TO CARBON
    • SNO : (MMFF number 18) SULFUR IN NITROGEN ANALOG OF A SULFONE
    • STHI : (MMFF number 44) SULFUR AS IN THIOPHENE
    • S-P : (MMFF number 72) TERMINAL SULFUR BONDED TO PHOSPHORUS
    • S2CM : (MMFF number 72) TERMINAL SULFUR IN THIOCARBOXYLATE ANION
    • SM : (MMFF number 72) TERMINAL SULFUR - FORMAL CHARGE=-1
    • SSMO : (MMFF number 72) TERMINAL SULFUR IN THIOSULFINATE GROUP
    • SO2M : (MMFF number 73) SULFUR IN NEGATIVELY CHARGED SULFINATE GROUP
    • SSOM : (MMFF number 73) TRICOORD SULFUR IN THIOSULFINATE GROUP
    • =S=O : (MMFF number 74) SULFINYL SULFUR, EG. IN C=S=O
    • Zinc
    • ZINC : (MMFF number 95) DIPOSITIVE ZINC
    • ZN+2 : (MMFF number 95) DIPOSITIVE ZINC
Coulombic interactions
    This force field uses point charges and has been set up to assign the point charges using the bond increment method. A nonzero base charge is applied to some atoms as noted in the atom descriptions seen above.
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Last updated: October 22, 2014