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MCCCS Towhee (OPLS-1996)

 

 

Overview
    This section covers the OPLS-1996 force field as it is implemented into the towhee_ff_OPLS-1996 file in the ForceFields directory. All of the Towhee atom types for this 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 this is a Lennard-Jones force field and can only be combined with other Lennard-Jones 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 the all-atom OPLS force fields were preceded by a united-atom version of the force field called OPLS-ua. There are several similar, but slightly different, versions of the OPLS all-atom forcefields implemented into Towhee. See OPLS-aa and OPLS-2001 for descriptions of these other versions. I would like to acknowledge W.L. Jorgensen for kindly providing me with an electronic copy of the OPLS-1996 parameters. Any discrepencies (especially typos) from the published OPLS-1996 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-1996 OPLS-1996 in Towhee
    The official force field name for OPLS-1996 in Towhee is 'OPLS-1996'. Here I list all of the atom names for use in the towhee_input file, along with a brief description taken from the electronic file. This file contains a mixture of united-atom and all-atom parameters. The Towhee name is a combination of the two letter descriptor and the integer count for each atom type provided in the electronic file. The capitalization and spacing pattern is important and must be followed exactly as listed here.
      Types 1-134 are from the united-atom force field. Some are needed for the UA solvents.
      Note: for UA amide parameters
      • NMA - types 1,2,3,4,7,39
      • formamide 131,2,12,13
      • DMF 131,2,3,132
      • acetamide 1,2,7,12,13
    • 'C -1' :
    • 'O -2' :
    • 'N -3' :
    • 'H -4' :
    • 'C2-5' :
    • 'CH-6' :
    • 'C3-7' :
    • 'CH-8' :
    • 'C2-9' :
    • 'C3-10' :
    • 'CD-11' :
    • 'N -12' :
    • 'H -13' :
    • 'CH-14' :
    • 'C2-15' :
    • 'C2-16' :
    • 'C -17' :
    • 'O2-18' :
    • 'C2-19' :
    • 'N3-20' :
    • 'H3-21' :
    • 'C2-22' :
    • 'OH-23' :
    • 'HO-24' :
    • 'CH-25' :
    • 'C -26' :
    • 'C2-27' :
    • 'C2-28' :
    • 'CH-29' :
    • 'CH-30' :
    • 'C2-31' :
    • 'SH-32' :
    • 'HS-33' :
    • 'C2-34' :
    • 'S -35' :
    • 'C3-36' :
    • 'C2-37' :
    • 'S -38' :
    • 'C3-39' :
    • 'NA-40' :
    • 'H -41' :
    • 'NB-42' :
    • 'CP-43' :
    • 'CF-44' :
    • 'CC-45' :
    • 'NA-46' :
    • 'H -47' :
    • 'CP-48' :
    • 'CG-49' :
    • 'CB-50' :
    • 'N2-51' :
    • 'H3-52' :
    • 'CA-53' :
    • 'N2-54' :
    • 'H3-55' :
    • 'C2-56' :
    • 'C2-57' :
    • 'C -58' : C in COOR ester JPC3315(91)
    • 'O -59' : O= in COOR ester
    • 'CH-60' :
    • 'C2-61' :
    • 'OS-62' : O- in COOR ester
    • 'C3-63' : CH3 in COOCH3
    • 'CT-64' :
    • 'C3-65' :
    • Types 66-77 JACS,106,6638 (1984)
    • 'C4-66' : CH4
    • 'C3-67' : CH3 (C1) ETHANE
    • 'C3-68' : CH3 (C2) N-ALKANES
    • 'C3-69' : CH3 (C3) ISOBUTANE
    • 'C3-70' : CH3 (C4) NEOPENTANE
    • 'C2-71' : CH2 (SP3) ALKANES
    • 'C9-72' : CH2 (SP2) 1-ALKENES
    • 'CH-73' : CH (SP3) ISOBUTANE
    • 'C8-74' : CH (SP2) 2-ALKENES
    • 'CD-75' : CH (AROM) BENZENOID united atom
    • 'CT-76' : C (SP3) NEOPENTANE
    • 'C7-77' : C (SP2) ISOBUTENE
    • 'OH-78' : O ALCOHOLS JPC,90,1276 (1986)
    • 'HO-79' : H(O) ALCOHOLS JPC,90,1276 (1986)
    • 'C3-80' : CH3 IN METHANOL JPC,90,1276 (1986)
    • 'C2-81' : CH2 IN ETHANOL JPC,90,1276 (1986)
    • 'SH-82' : S IN H2S JPC,90,6379 (1986)
    • 'SH-83' : S IN RSH JPC,90,6379 (1986)
    • 'S -84' : S IN RSR JPC,90,6379 (1986)
    • 'S -85' : S IN RSSR JPC,90,6379 (1986)
    • 'HS-86' : H IN H2S JPC,90,6379 (1986)
    • 'HS-87' : H(S) IN RSH JPC,90,6379 (1986)
    • 'C3-88' : CH3 IN CH2SH JPC,90,6379 (1986)
    • 'C2-89' : CH2 IN CH3CHSSH JPC,90,6379 (1986)
    • 'C3-90' : CH3 IN CH3SR JPC,90,6379 (1986)
    • 'C2-91' : CH2 IN RCH2SR JPC,90,6379 (1986)
    • 'C3-92' : CH3 IN CH3SSR JPC,90,6379 (1986)
    • 'C2-93' : CH2 IN RCH2SSR JPC,90,6379 (1986)
    • 'Ar-97' : Ar - Verlet & Weis, Mol Phys. 24,1013 (1972)
    • 'Kr-98' : Kr - Verlet & Weis, Mol Phys. 24,1013 (1972)
    • 'Xe-99' : Xe - Verlet & Weis, Mol Phys. 24,1013 (1972)
    • 'N3-101' : N (NH4+) JPC,90,2174 (1986)
    • 'N3-102' : N (RNH3+) JPC,90,2174 (1986)
    • 'H3-104' : H (NH4+) JPC,90,2174 (1986)
    • 'H3-105' : H (RNH3+) JPC,90,2174 (1986)
    • 'C3-106' : CH3 (CH3NH3+) JPC,90,2174 (1986) United-atom
    • 'C3-107' : CH3 ((CH3)4N+) JPC,90,2174 (1986) United-atom
    • 'OS-108' : ETHER O JCC,11,958 (1990)
    • 'C3-109' : ETHER CH3 (-O) JCC,11,958 (1990)
    • 'C2-110' : ETHER CH2 (-O) JCC,11,958 (1990)
    • 'C2-118' : CH2 Methylenechloride C-CL = 1.772
    • 'Cl-119' : Cl Methylenechloride Cl-C-Cl = 111.8
    • 'CH-120' : CH Chloroform JPC,94,1683 (1990)
    • 'Cl-121' : Cl Chloroform C-Cl = 1.758 Cl-C-Cl = 111.3
    • 'CT-122' : C CCl4
    • 'Cl-123' : Cl CCl4
    • 'Ne-129' : Neon - Hirschfelder (Wiley,1954)
    • 'He-130' : Helium - Hirschfelder (Wiley,1954)
    • 'C -131' : C in C=O for UA formamide, DMF
    • 'C3-132' : CH3 in HCON(CH3)2 DMF
    • All-atom parameters start at 135.
    • 'CT-135' : CH3 all-atom C: alkanes
    • 'CT-136' : CH2 all-atom C: alkanes
    • 'CT-137' : CH all-atom C: alkanes
    • 'CT-138' : CH4 all-atom C: methane
    • 'CT-139' : C all-atom C: alkanes
    • 'HC-140' : H all-atom H: alkanes
    • 'CM-141' : alkene C (R2-C=) all atom
    • 'CM-142' : alkene C (RH-C=) all atom
    • 'CM-143' : alkene C (H2-C=) all atom
    • 'HC-144' : alkene H (H-C=) all atom
    • 'CA-145' : Benzene C - 12 site JACS, 112, 4768-90
    • 'HA-146' : Benzene H - 12 site
    • 'CA-147' : Naphthalene fusion C (C9)
    • 'CT-148' : all-atom C: CH3, toluene
    • 'CT-149' : all -atom C: CH2, ethyl benzene
    • 'OH-154' : all-atom O: mono alcohols
    • 'HO-155' : all-atom H(O): mono alcohols
    • 'HC-156' : all-atom H(C): methanol
    • 'CT-157' : all-atom C: CH3 & CH2, alcohols
    • 'CT-158' : all-atom C: CH, alcohols
    • 'CT-159' : all-atom C: C, alcohols
    • 'CT-160' : CH2 Trifluoroethanol
    • 'CT-161' : CF3 Trifluoroethanol
    • 'OH-162' : OH Trifluoroethanol
    • 'HO-163' : HO Trifluoroethanol
    • 'F -164' : F Trifluoroethanol
    • 'HC-165' : H Trifluoroethanol
    • 'CA-166' : C(OH) phenol Use with all atom C, H 145 & 146
    • 'OH-167' : O phenol Use with all atom C, H 145 & 146
    • 'HO-168' : H phenol Use with all atom C, H 145 & 146
    • 'OH-169' : O: diols
    • 'HO-170' : H(O) diols
    • 'OS-180' : O: ether
    • 'CT-181' : C(H3OR): methyl ether
    • 'CT-182' : C(H2OR): ethyl ether
    • 'CT-183' : C(HOR): i-Pr ether
    • 'CT-184' : C(OR): t-Bu ether
    • 'HC-185' : H(COR): alpha H ether
    • 'OS-186' : O: acetal
    • 'OH-187' : O(H): hemiacetal
    • 'HO-188' : H(O): hemiacetal
    • 'CO-189' : C(H2O2): acetal OCH2O
    • 'HC-190' : H(CHO2): acetal OCH2O
    • 'CO-191' : C(H2O2): hemiacetal OCH2OH
    • 'HC-192' : H(CHO2): hemiacetal OCH2OH
    • 'CO-193' : C(HCO2): acetal OCHRO
    • 'HC-194' : H(CHO2): acetal OCHRO
    • 'CO-195' : C(HCO2): hemiacetal OCHROH
    • 'HC-196' : H(C2O2): hemiacetal OCHROH
    • 'CO-197' : C(C2O2): acetal OCRRO
    • 'CO-198' : C(C2O2): hemiacetal OCRROH
    • 'SH-200' : all-atom S: thiols
    • 'SH-201' : S IN H2S JPC,90,6379 (1986)
    • 'S -202' : all-atom S: sulfides
    • 'S -203' : all-atom S: disulfides
    • 'HS-204' : all-atom H(S): thiols
    • 'HS-205' : H IN H2S JPC,90,6379 (1986)
    • 'CT-206' : all-atom C: CH2, thiols
    • 'CT-207' : all-atom C: CH, thiols
    • 'CT-208' : all-atom C: C, thiols
    • 'CT-209' : all-atom C: CH3, sulfides
    • 'CT-210' : all-atom C: CH2, sulfides
    • 'CT-211' : all-atom C: CH, sulfides
    • 'CT-212' : all-atom C: C, sulfides
    • 'CT-213' : all-atom C: CH3, disulfides
    • 'CT-214' : all-atom C: CH2, disulfides
    • 'CT-215' : all-atom C: CH, disulfides
    • 'CT-216' : all-atom C: C, disulfides
    • 'NT-220' : N in RNH2 amine JPC,94,1683 (1990)
    • 'H2-221' : H in RNH2 amine
    • 'CT-222' : C in CH3NH2; H on C is type 140
    • 'CT-223' : C in RCH2NH2 and Gly CA
    • 'CT-224' : C in R2CHNH2 and Ala CA
    • 'CT-225' : C in R3CNH2 and Aib CA
    • 'CA-226' : C(NH2) aniline
    • 'NT-227' : N aniline
    • 'H2-228' : H(N) aniline
    • 'NT-229' : N in R3N trimethylamine
    • 'CT-230' : C in RCH2NRR H on C is type 140
    • 'CT-231' : C in RN(CH3)2 H on C is type 140
    • 'C -235' : C: C=O in amide. Acyl R in amides is neutral - use alkane parameters.
    • 'O -236' : O: C=O in amide. Acyl R in amides is neutral - use alkane parameters.
    • 'N -237' : N: primary amide.
    • 'N -238' : N: secondary amide
    • 'N -239' : N: tertiary amide
    • 'H -240' : H on N: primary amide
    • 'H -241' : H on N: secondary amide
    • 'CT-242' : C on N: secondary N-Me amide
    • 'CT-243' : C on N: tertiary N-Me amide
    • 'CT-244' : C on N: secondary N-CH2R amide
    • 'CT-245' : C on N: tertiary N-CH2R amide (Pro Cdelta)
    • 'CT-246' : C on N: tertiary N-CHR2 amide (Pro Calpha)
    • 'C -247' : C in O=C(NH2)2 Urea
    • 'O -248' : O in O=C(NHw)w Urea Isr. J. Chem. 33, 323 (93)
    • 'N -249' : N in O=C(NH2)2 Urea Isr. J. Chem. 33, 323 (93)
    • 'H -250' : H in O=C(NH2)2 Urea
    • 'N -251' : N in imide
    • 'C -252' : C(=O) in imide
    • 'O -253' : O in imide
    • 'H -254' : H(N) in imide
    • 'HC-255' : H(C) in formimide
    • 'CT-256' : C in CH3 imide
    • 'CT-257' : C in RCH2 imide
    • 'CT-258' : C in R2CH imide
    • 'CT-259' : C in R3C imide
    • 'C -267' : Co in CCOOH carboxylic acid
    • 'OH-268' : Oh in CCOOH: R in RCOOH is neutral; use 135-140
    • 'O -269' : Oc in CCOOH
    • 'HO-270' : H in CCOOH
    • 'C -271' : C in COO- carboxylate
    • 'O2-272' : O: O in COO- carboxylate
    • 'CT-273' : C: CH3, carboxylate ion
    • 'CT-274' : C: CH2, carboxylate ion
    • 'CT-275' : C: CH, carboxylate ion
    • 'CT-276' : C: C, carboxylate ion
    • 'C -277' : AA C: aldehyde - for C-alpha use 135-139
    • 'O -278' : AA O: aldehyde
    • 'HC-279' : AA H-alpha in aldehyde & formamide
    • 'C -280' : AA C: ketone - for C-alpha use 135-139
    • 'O -281' : AA O: ketone
    • 'HC-282' : AA H on C-alpha in ketone & aldehyde
    • 'N3-286' : N (NH4+) JPC,90,2174 (1986)
    • 'N3-287' : N (RNH3+) JPC,90,2174 (1986)
    • 'H3-289' : H (NH4+) JPC,90,2174 (1986)
    • 'H3-290' : H (RNH3+) JPC,90,2174 (1986)
    • 'CT-291' : C in CH3NH3+
    • 'CT-292' : C in RCH2NH3+
    • 'CT-293' : C in R2CHNH3+
    • 'CT-294' : C in R3CNH3+
    • 'N2-300' : N: guanidinium NH2
    • 'H3-301' : H: guanidinium NH2
    • 'CA-302' : C: guanidinum C+
    • 'N2-303' : N: guanidinium NHR
    • 'H3-304' : H: guanidinium NHR
    • 'CT-305' : C: CH3, methylguanidinium
    • 'CT-306' : C: CH3, ethylguanidinium
    • 'CT-307' : C: CH2(D), ARG,ethylguanidinium
    • 'CT-308' : C: CH2(G), ARG
    • 'NA-311' : DAP N1 Diamino-pyridine
    • 'CA-312' : DAP C2 Diamino-pyridine
    • 'N2-313' : DAP N-amine
    • 'H2-314' : DAP H-amine
    • 'CA-315' : DAP C3
    • 'HC-316' : DAP H3
    • 'CA-317' : DAP C4
    • 'HC-318' : DAP H4
    • 'NA-319' : Uracil N1 - use AT=N* for nucleoside
    • 'C -320' : Uracil C2
    • 'NA-321' : Uracil N3
    • 'C -322' : Uracil C4
    • 'CM-323' : Uracil C5
    • 'CM-324' : Uracil C6
    • 'H -325' : Uracil H-N1
    • 'O -326' : Uracil O-C2
    • 'H -327' : Uracil H-N3
    • 'O -328' : Uracil O-C4
    • 'HC-329' : Uracil H-C5
    • 'HC-330' : Uracil H-C6
    • 'CT-331' : Thymine C-C5
    • 'HC-332' : Thymine H-CC5
    • 'NA-333' : Cytosine N1 - use AT=N* for nucleoside
    • 'C -334' : Cytosine C2
    • 'NC-335' : Cytosine N3
    • 'CA-336' : Cytosine C4 Nucleotide base parameters: JACS 113,2810 (1991)
    • 'CA-337' : Cytosine C5
    • 'CM-338' : Cytosine C6
    • 'H -339' : Cytosine H-N1
    • 'O -340' : Cytosine O-C2
    • 'N2-341' : Cytosine N-C4
    • 'H2-342' : Cytosine H-NC4/N3
    • 'H2-343' : Cytosine H-NC4/C5
    • 'HC-344' : Cytosine H-C5
    • 'HC-345' : Cytosine H-C6
    • 'NC-346' : Adenine N1
    • 'CQ-347' : Adenine C2
    • 'NC-348' : Adenine N3
    • 'CB-349' : Adenine C4
    • 'CB-350' : Adenine C5
    • 'CA-351' : Adenine C6
    • 'NB-352' : Adenine N7 Guanine
    • 'CK-353' : Adenine C8 Guanine
    • 'NA-354' : Adenine N9 Guanine - use AT=N* for nucleoside
    • 'HC-355' : Adenine H-C2
    • 'N2-356' : Adenine N-C6
    • 'H2-357' : Adenine H-NC6/N1
    • 'H2-358' : Adenine H-NC6/C5
    • 'HC-359' : Adenine H-C8 Guanine
    • 'H -360' : Adenine H-N9 Guanine
    • 'NA-361' : Guanine N1
    • 'CA-362' : Guanine C2
    • 'NC-363' : Guanine N3
    • 'CB-364' : Guanine C4
    • 'CB-365' : Guanine C5
    • 'C -366' : Guanine C6
    • 'H -367' : Guanine H-N1
    • 'N2-368' : Guanine N-C2
    • 'H2-369' : Guanine H-NC2
    • 'O -370' : Guanine O-C6
    • 'CT-371' : 9-Me A or G C-N9
    • 'HC-372' : 9-Me A or G H-CN9
    • 'CT-373' : 1-Me U or T C-N1
    • 'HC-374' : 1-Me U or T H-CN1
    • 'CT-375' : 1-Me Cytosine C-N1
    • 'HC-376' : 1-Me Cytosine H-CN1
    • 'NA-377' : CytH+ N1 Use AT=N* for nucleoside.
    • 'C -378' : CytH+ C2
    • 'NA-379' : CytH+ N3 Protonated cytosine.
    • 'CA-380' : CytH+ C4
    • 'CM-381' : CytH+ C5
    • 'CM-382' : CytH+ C6
    • 'H -383' : CytH+ H-N1
    • 'O -384' : CytH+ O-C2
    • 'H -385' : CythH+ H-N3
    • 'N2-386' : CytH+ N-C4
    • 'H2-387' : CytH+ H-NC4/N3
    • 'H2-388' : CytH+ H-NC4/C5
    • 'HC-389' : CytH+ H-C5
    • 'HC-390' : CytH+ H-C6
    • 'CT-391' : 1-Me CytH+ C-N1
    • 'HC-392' : 1-Me CytH+ H-CN1
    • 'P -393' : P dimethylphosphate anion
    • 'O2-394' : O(=) dimethylphosphate anion
    • 'OS-395' : O(-) dimethylphosphate anion
    • 'CT-396' : C in CH3 dimethylphosphate anion
    • 'F -400' : F- JACS 106,903 (1984)
    • 'Cl-401' : Cl- JACS 106, 903 (1984)
    • 'Br-402' : Br- JACS 107, 7793 (1985)
    • 'Li-404' : Li+ JACS 106, 903 (1984)
    • 'Na-405' : Na+ JACS 106, 903 (1984)
    • 'Li-406' : Li+ Aqvist's cation parameters: JPC,94,8021 (90)
    • 'Na-407' : Na+ Aqvist's cation parameters: JPC,94,8021 (90)
    • 'K -408' : K+ Aqvist's cation parameters: JPC,94,8021 (90)
    • 'Rb-409' : Rb+ Aqvist's cation parameters: JPC,94,8021 (90)
    • 'Cs-410' : Cs+ Aqvist's cation parameters: JPC,94,8021 (90)
    • 'Mg-411' : Mg++ Aqvist's cation parameters: JPC,94,8021 (90)
    • 'Ca-412' : Ca++ Aqvist's cation parameters: JPC,94,8021 (90)
    • 'Sr-413' : Sr++ Aqvist's cation parameters: JPC,94,8021 (90)
    • 'Ba-414' : Ba++ Aqvist's cation parameters: JPC,94,8021 (90)
    • 'O -434' : O in OH- Hydroxide O-H = 0.953A
    • 'HO-435' : H in OH- JACS 108,2517 (86)
    • 'U -436' : U in UO2+ J. Mol. Struct. 366, 55 (96)
    • 'OU-437' : O in UO2+ r(U-O) = 1.80 A
    • 'CA-500' : CG in Trp
    • 'CA-501' : CD C in Trp
    • 'CA-502' : CE C in Trp
    • 'NA-503' : NE in Trp
    • 'H -504' : H on NE in Trp
    • 'CT-505' : CB in His
    • 'CA-506' : CE1 in HID,HIE
    • 'CA-507' : CD2 in HID, CG in HIE
    • 'CA-508' : CG in HID, CD2 in HIE
    • 'CA-509' : CE1 in HIP
    • 'CA-510' : CG, CD2 in HIP
    • 'NB-511' : NE in HID, ND in HIE
    • 'NA-512' : N in HIP
    • 'H -513' : H on N in HIP
Coulombic interactions
    OPLS-1996 uses atom-centered point charges to represent the electrostatic interactions. Each of the atom types listed above has a default charge suggested by the forcefield and you can use these default charges by using the 'bond increment' option.
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
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Send comments to: Marcus G. Martin
Last updated: July 18, 2006