; ######################################################################## ; # # ; # ffamber ports for GROMACS 3.3.1 - August 2007 # ; # Eric J. Sorin - CSU Long Beach, Dept. of Chem & Biochem # ; # With significant contributions from Sanghyun Park and Jory Z. Ruscio # ; # Please cite: Sorin & Pande (2005). Biophys. J. 88(4), 2472-2493. # ; # For additional information, tools, and updates # ; # please consult http://chemistry.csulb.edu/ffamber/ # ; # # ; ######################################################################## [ bondtypes ] ; i j func b0 kb CT H0 1 0.10900 284512.0 ; 03GLY changed from 331 bsd on NMA nmodes; AA, SUGARS C C 1 0.1525 259408.0 ; new99 C OS 1 0.1323 376560.0 ; new99 C H4 1 0.1080 307105.6 ; new99 C H5 1 0.1080 307105.6 ; new99 CA OH 1 0.1364 376560.0 ; new99 CM OS 1 0.1240 401664.0 ; new99 Cl CT 1 0.1766 194137.6 ; new99 Br CT 1 0.1944 133051.2 ; new99 I CT 1 0.2166 123846.4 ; new99 F CA 1 0.1359 323004.8 ; new99 Cl CA 1 0.1727 161502.4 ; new99 I CA 1 0.2075 143092.8 ; new99 Br CA 1 0.1890 143929.6 ; new99 OW HW 1 0.09572 462750.4 ; P water HW HW 1 0.15136 462750.4 ; P water C CA 1 0.14090 392459.2 ; 7,(1986),230; TYR C CB 1 0.14190 374049.6 ; 7,(1986),230; GUA C CM 1 0.14440 343088.0 ; 7,(1986),230; THY,URA C CT 1 0.15220 265265.6 ; 7,(1986),230; AA C N* 1 0.13830 354803.2 ; 7,(1986),230; CYT,URA C NA 1 0.13880 349782.4 ; 7,(1986),230; GUA.URA C NC 1 0.13580 382417.6 ; 7,(1986),230; CYT C O 1 0.12290 476976.0 ; 7,(1986),230; AA,CYT,GUA,THY,URA C O2 1 0.12500 548940.8 ; 7,(1986),230; GLU,ASP C OH 1 0.13640 376560.0 ; 7,(1986),230; TYR CA CA 1 0.14000 392459.2 ; 7,(1986),230; BENZENE,PHE,TRP,TYR CA CB 1 0.14040 392459.2 ; 7,(1986),230; ADE,TRP CA CM 1 0.14330 357313.6 ; 7,(1986),230; CYT CA CT 1 0.15100 265265.6 ; 7,(1986),230; PHE,TYR CA HA 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes; PHE,TRP,TYR CA H4 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes; no assigned CA N2 1 0.13400 402500.8 ; 7,(1986),230; ARG,CYT,GUA CA NA 1 0.13810 357313.6 ; 7,(1986),230; GUA CA NC 1 0.13390 404174.4 ; 7,(1986),230; ADE,CYT,GUA CB CB 1 0.13700 435136.0 ; 7,(1986),230; ADE,GUA CB N* 1 0.13740 364844.8 ; 7,(1986),230; ADE,GUA CB NB 1 0.13910 346435.2 ; 7,(1986),230; ADE,GUA CB NC 1 0.13540 385764.8 ; 7,(1986),230; ADE,GUA CK H5 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes; ADE,GUA CK N* 1 0.13710 368192.0 ; 7,(1986),230; ADE,GUA CK NB 1 0.13040 442667.2 ; 7,(1986),230; ADE,GUA CM CM 1 0.13500 459403.2 ; 7,(1986),230; CYT,THY,URA CM CT 1 0.15100 265265.6 ; 7,(1986),230; THY CM HA 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes; CYT,URA CM H4 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes; CYT,URA CM H5 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes; not assigned CM N* 1 0.13650 374886.4 ; 7,(1986),230; CYT,THY,URA CQ H5 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes; ADE CQ NC 1 0.13240 420073.6 ; 7,(1986),230; ADE CT CT 1 0.15260 259408.0 ; 7,(1986),230; AA, SUGARS CT HC 1 0.10900 284512.0 ; ged from 331 bsd on NMA nmodes; AA, SUGARS CT H1 1 0.10900 284512.0 ; ged from 331 bsd on NMA nmodes; AA, RIBOSE CT H2 1 0.10900 284512.0 ; ged from 331 bsd on NMA nmodes; SUGARS CT H3 1 0.10900 284512.0 ; ged from 331 bsd on NMA nmodes; not assigned CT HP 1 0.10900 284512.0 ; nged from 331; AA-lysine, methyl ammonium cation CT N* 1 0.14750 282001.6 ; 7,(1986),230; ADE,CYT,GUA,THY,URA CT N2 1 0.14630 282001.6 ; 7,(1986),230; ARG CT OH 1 0.14100 267776.0 ; 7,(1986),230; SUGARS CT OS 1 0.14100 267776.0 ; 7,(1986),230; NUCLEIC ACIDS H N2 1 0.10100 363171.2 ; 7,(1986),230; ADE,CYT,GUA,ARG H N* 1 0.10100 363171.2 ; plain unmethylated bases ADE,CYT,GUA,ARG H NA 1 0.10100 363171.2 ; 7,(1986),230; GUA,URA,HIS HO OH 1 0.09600 462750.4 ; 7,(1986),230; SUGARS,SER,TYR HO OS 1 0.09600 462750.4 ; 7,(1986),230; NUCLEOTIDE ENDS O2 P 1 0.14800 439320.0 ; 7,(1986),230; NA PHOSPHATES OH P 1 0.16100 192464.0 ; 7,(1986),230; NA PHOSPHATES OS P 1 0.16100 192464.0 ; 7,(1986),230; NA PHOSPHATES C* HC 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes, not needed AA C N 1 0.13350 410032.0 ; 7,(1986),230; AA C* CB 1 0.14590 324678.4 ; 7,(1986),230; TRP C* CT 1 0.14950 265265.6 ; 7,(1986),230; TRP C* CW 1 0.13520 456892.8 ; 7,(1986),230; TRP CA CN 1 0.14000 392459.2 ; 7,(1986),230; TRP CB CN 1 0.14190 374049.6 ; 7,(1986),230; TRP CC CT 1 0.15040 265265.6 ; 7,(1986),230; HIS CC CV 1 0.13750 428441.6 ; 7,(1986),230; HIS(delta) CC CW 1 0.13710 433462.4 ; 7,(1986),230; HIS(epsilon) CC NA 1 0.13850 353129.6 ; 7,(1986),230; HIS CC NB 1 0.13940 343088.0 ; 7,(1986),230; HIS CN NA 1 0.13800 358150.4 ; 7,(1986),230; TRP CR H5 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes;HIS CR NA 1 0.13430 399153.6 ; 7,(1986),230; HIS CR NB 1 0.13350 408358.4 ; 7,(1986),230; HIS CT N 1 0.14490 282001.6 ; 7,(1986),230; AA CT N3 1 0.14710 307105.6 ; 7,(1986),230; LYS CT S 1 0.18100 189953.6 ; ged from 222.0 based on dimethylS nmodes CT SH 1 0.18100 198321.6 ; ged from 222.0 based on methanethiol nmodes CV H4 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes; HIS CV NB 1 0.13940 343088.0 ; 7,(1986),230; HIS CW H4 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes;HIS(epsilon,+) CW NA 1 0.13810 357313.6 ; 7,(1986),230; HIS,TRP H N 1 0.10100 363171.2 ; 7,(1986),230; AA H N3 1 0.10100 363171.2 ; 7,(1986),230; LYS HS SH 1 0.13360 229283.2 ; 7,(1986),230; CYS S S 1 0.20380 138908.8 ; 7,(1986),230; CYX (SCHERAGA) CT F 1 0.13800 307105.6 ; 13,(1992),963;CF4; R0=1.332 FOR CHF3 [ angletypes ] ; i j k func th0 cth H0 CT H0 1 109.500 292.880 ; 03GLY H0 CT N 1 109.500 418.400 ; 03GLY AA general changed based on NMA nmodes C CT H0 1 109.500 418.400 ; 03GLY AA general changed based on NMA nmodes HW OW HW 1 104.520 836.800 ; TIP3P water HW HW OW 1 127.740 0.000 ; (found in crystallographic water with 3 bonds) C C O 1 120.000 669.440 ; new99 C C OH 1 120.000 669.440 ; new99 CT C CT 1 117.000 527.184 ; new99 CT C OS 1 115.000 669.440 ; new99 O C OS 1 125.000 669.440 ; new99 H4 C C 1 120.000 418.400 ; new99 H4 C CM 1 115.000 418.400 ; new99 H4 C CT 1 115.000 418.400 ; new99 H4 C O 1 120.000 418.400 ; new99 H4 C OH 1 120.000 418.400 ; new99 H5 C N 1 120.000 418.400 ; new99 H5 C O 1 119.000 418.400 ; new99 H5 C OH 1 107.000 418.400 ; new99 H5 C OS 1 107.000 418.400 ; new99 CA CA OH 1 120.000 585.760 ; new99 CA OH HO 1 113.000 418.400 ; new99 F CA CA 1 121.000 585.760 ; new99 Cl CA CA 1 118.800 585.760 ; new99 Br CA CA 1 118.800 585.760 ; new99 I CA CA 1 118.800 585.760 ; new99 CM CM OS 1 125.000 669.440 ; new99 H4 CM OS 1 113.000 418.400 ; new99 HA CM HA 1 120.000 292.880 ; new99 HA CM CT 1 120.000 418.400 ; new99 H1 CT CM 1 109.500 418.400 ; new99 HC CT CM 1 109.500 418.400 ; new99 C CT OS 1 109.500 502.080 ; new99 CM CT CT 1 111.000 527.184 ; new99 CM CT OS 1 109.500 418.400 ; new99 CT CT CA 1 114.000 527.184 ; new99 OS CT OS 1 101.000 502.080 ; new99 F CT CT 1 109.000 418.400 ; new99 F CT H2 1 109.500 418.400 ; new99 Cl CT CT 1 108.500 418.400 ; new99 Cl CT H1 1 108.500 418.400 ; new99 Br CT CT 1 108.000 418.400 ; new99 Br CT H1 1 106.500 418.400 ; new99 I CT CT 1 106.000 418.400 ; new99 CB C NA 1 111.300 585.760 ; NA CB C O 1 128.800 669.440 ; CM C NA 1 114.100 585.760 ; CM C O 1 125.300 669.440 ; CT C O 1 120.400 669.440 ; CT C O2 1 117.000 585.760 ; CT C OH 1 110.000 669.440 ; new99 N* C NA 1 115.400 585.760 ; N* C NC 1 118.600 585.760 ; N* C O 1 120.900 669.440 ; NA C O 1 120.600 669.440 ; NC C O 1 122.500 669.440 ; CT C N 1 116.600 585.760 ; AA general N C O 1 122.900 669.440 ; AA general O C O 1 126.000 669.440 ; AA COO- terminal residues O2 C O2 1 126.000 669.440 ; AA GLU (SCH JPC 79,2379) O C OH 1 120.000 669.440 ; CA C CA 1 120.000 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA tyr CA C OH 1 120.000 585.760 ; AA tyr C CA CA 1 120.000 527.184 ; changed from 85.0 bsd on C6H6 nmodes CA CA CA 1 120.000 527.184 ; changed from 85.0 bsd on C6H6 nmodes CA CA CB 1 120.000 527.184 ; changed from 85.0 bsd on C6H6 nmodes CA CA CT 1 120.000 585.760 ; CA CA HA 1 120.000 418.400 ; new99 CA CA H4 1 120.000 418.400 ; new99 CB CA HA 1 120.000 418.400 ; new99 CB CA H4 1 120.000 418.400 ; new99 CB CA N2 1 123.500 585.760 ; CB CA NC 1 117.300 585.760 ; CM CA N2 1 120.100 585.760 ; CM CA NC 1 121.500 585.760 ; N2 CA NA 1 116.000 585.760 ; N2 CA NC 1 119.300 585.760 ; NA CA NC 1 123.300 585.760 ; C CA HA 1 120.000 418.400 ; new99 tyr N2 CA N2 1 120.000 585.760 ; AA arg CN CA HA 1 120.000 418.400 ; new99 trp CA CA CN 1 120.000 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA trp C CB CB 1 119.200 527.184 ; changed from 85.0 bsd on C6H6 nmodes; NA gua C CB NB 1 130.000 585.760 ; CA CB CB 1 117.300 527.184 ; changed from 85.0 bsd on C6H6 nmodes; NA ade CA CB NB 1 132.400 585.760 ; CB CB N* 1 106.200 585.760 ; CB CB NB 1 110.400 585.760 ; CB CB NC 1 127.700 585.760 ; N* CB NC 1 126.200 585.760 ; C* CB CA 1 134.900 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA trp C* CB CN 1 108.800 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA trp CA CB CN 1 116.200 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA trp H5 CK N* 1 123.050 418.400 ; new99 H5 CK NB 1 123.050 418.400 ; new99 N* CK NB 1 113.900 585.760 ; C CM CM 1 120.700 527.184 ; changed from 85.0 bsd on C6H6 nmodes; NA thy C CM CT 1 119.700 585.760 ; C CM HA 1 119.700 418.400 ; new99 C CM H4 1 119.700 418.400 ; new99 CA CM CM 1 117.000 527.184 ; changed from 85.0 bsd on C6H6 nmodes; NA cyt CA CM HA 1 123.300 418.400 ; new99 CA CM H4 1 123.300 418.400 ; new99 CM CM CT 1 119.700 585.760 ; CM CM HA 1 119.700 418.400 ; new99 CM CM H4 1 119.700 418.400 ; new99 CM CM N* 1 121.200 585.760 ; H4 CM N* 1 119.100 418.400 ; new99 H5 CQ NC 1 115.450 418.400 ; new99 NC CQ NC 1 129.100 585.760 ; CM CT HC 1 109.500 418.400 ; changed based on NMA nmodes CT CT CT 1 109.500 334.720 ; CT CT HC 1 109.500 418.400 ; changed based on NMA nmodes CT CT H1 1 109.500 418.400 ; changed based on NMA nmodes CT CT H2 1 109.500 418.400 ; changed based on NMA nmodes CT CT HP 1 109.500 418.400 ; changed based on NMA nmodes CT CT N* 1 109.500 418.400 ; CT CT OH 1 109.500 418.400 ; CT CT OS 1 109.500 418.400 ; HC CT HC 1 109.500 292.880 ; H1 CT H1 1 109.500 292.880 ; HP CT HP 1 109.500 292.880 ; AA lys, ch3nh4+ H2 CT N* 1 109.500 418.400 ; changed based on NMA nmodes H1 CT N* 1 109.500 418.400 ; changed based on NMA nmodes H1 CT OH 1 109.500 418.400 ; changed based on NMA nmodes H1 CT OS 1 109.500 418.400 ; changed based on NMA nmodes H2 CT OS 1 109.500 418.400 ; changed based on NMA nmodes N* CT OS 1 109.500 418.400 ; H1 CT N 1 109.500 418.400 ; AA general changed based on NMA nmodes C CT H1 1 109.500 418.400 ; AA general changed based on NMA nmodes C CT HP 1 109.500 418.400 ; AA zwitterion changed based on NMA nmodes H1 CT S 1 109.500 418.400 ; AA cys changed based on NMA nmodes H1 CT SH 1 109.500 418.400 ; AA cyx changed based on NMA nmodes CT CT S 1 114.700 418.400 ; AA cyx (SCHERAGA JPC 79,1428) CT CT SH 1 108.600 418.400 ; AA cys H2 CT H2 1 109.500 292.880 ; AA lys H1 CT N2 1 109.500 418.400 ; AA arg changed based on NMA nmodes HP CT N3 1 109.500 418.400 ; AA lys, ch3nh3+, changed based on NMA nmodes CA CT CT 1 114.000 527.184 ; AA phe tyr (SCH JPC 79,2379) C CT HC 1 109.500 418.400 ; AA gln changed based on NMA nmodes C CT N 1 110.100 527.184 ; AA general CT CT N2 1 111.200 669.440 ; AA arg (JCP 76, 1439) CT CT N 1 109.700 669.440 ; AA ala, general (JACS 94, 2657) C CT CT 1 111.100 527.184 ; AA general CA CT HC 1 109.500 418.400 ; AA tyr changed based on NMA nmodes CT CT N3 1 111.200 669.440 ; AA lys (JCP 76, 1439) CC CT CT 1 113.100 527.184 ; AA his CC CT HC 1 109.500 418.400 ; AA his changed based on NMA nmodes C CT N3 1 111.200 669.440 ; AA amino terminal residues C* CT CT 1 115.600 527.184 ; AA trp C* CT HC 1 109.500 418.400 ; AA trp changed based on NMA nmodes CT CC NA 1 120.000 585.760 ; AA his CT CC CV 1 120.000 585.760 ; AA his CT CC NB 1 120.000 585.760 ; AA his CV CC NA 1 120.000 585.760 ; AA his CW CC NA 1 120.000 585.760 ; AA his CW CC NB 1 120.000 585.760 ; AA his CT CC CW 1 120.000 585.760 ; AA his H5 CR NA 1 120.000 418.400 ; new99 his H5 CR NB 1 120.000 418.400 ; new99 his NA CR NA 1 120.000 585.760 ; AA his NA CR NB 1 120.000 585.760 ; AA his CC CV H4 1 120.000 418.400 ; new99 his CC CV NB 1 120.000 585.760 ; AA his H4 CV NB 1 120.000 418.400 ; new99 his CC CW H4 1 120.000 418.400 ; new99 his CC CW NA 1 120.000 585.760 ; AA his H4 CW NA 1 120.000 418.400 ; new99 his C* CW H4 1 120.000 418.400 ; new99 trp C* CW NA 1 108.700 585.760 ; AA trp CT C* CW 1 125.000 585.760 ; AA trp CB C* CT 1 128.600 585.760 ; AA trp CB C* CW 1 106.400 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA trp CA CN NA 1 132.800 585.760 ; AA trp CB CN NA 1 104.400 585.760 ; AA trp CA CN CB 1 122.700 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA trp C N CT 1 121.900 418.400 ; AA general C N H 1 120.000 418.400 ; new99 general, gln, asn,changed based on NMA nmodes CT N H 1 118.040 418.400 ; new99 general, changed based on NMA nmodes CT N CT 1 118.000 418.400 ; AA pro (DETAR JACS 99,1232) H N H 1 120.000 292.880 ; ade,cyt,gua,gln,asn ** C N* CM 1 121.600 585.760 ; C N* CT 1 117.600 585.760 ; C N* H 1 119.200 418.400 ; new99 CB N* CK 1 105.400 585.760 ; CB N* CT 1 125.800 585.760 ; CB N* H 1 125.800 418.400 ; new99 CK N* CT 1 128.800 585.760 ; CK N* H 1 128.800 418.400 ; new99 for unmethylated n.a. bases,chngd bsd NMA nmodes CM N* CT 1 121.200 585.760 ; CM N* H 1 121.200 418.400 ; new99 for unmethylated n.a. bases,chngd bsd NMA nmodes CA N2 H 1 120.000 418.400 ; new99 H N2 H 1 120.000 292.880 ; CT N2 H 1 118.400 418.400 ; new99 arg CA N2 CT 1 123.200 418.400 ; AA arg CT N3 H 1 109.500 418.400 ; AA lys, changed based on NMA nmodes CT N3 CT 1 109.500 418.400 ; AA pro/nt H N3 H 1 109.500 292.880 ; AA lys, AA(end) C NA C 1 126.400 585.760 ; C NA CA 1 125.200 585.760 ; C NA H 1 116.800 418.400 ; new99 CA NA H 1 118.000 418.400 ; new99 CC NA CR 1 120.000 585.760 ; AA his CC NA H 1 120.000 418.400 ; new99 his CR NA CW 1 120.000 585.760 ; AA his CR NA H 1 120.000 418.400 ; new99 his CW NA H 1 120.000 418.400 ; new99 his CN NA CW 1 111.600 585.760 ; AA trp CN NA H 1 123.100 418.400 ; new99 trp CB NB CK 1 103.800 585.760 ; CC NB CR 1 117.000 585.760 ; AA his CR NB CV 1 117.000 585.760 ; AA his C NC CA 1 120.500 585.760 ; CA NC CB 1 112.200 585.760 ; CA NC CQ 1 118.600 585.760 ; CB NC CQ 1 111.000 585.760 ; C OH HO 1 113.000 418.400 ; new99 CT OH HO 1 108.500 460.240 ; HO OH P 1 108.500 376.560 ; CT OS CT 1 109.500 502.080 ; CT OS P 1 120.500 836.800 ; P OS P 1 120.500 836.800 ; O2 P OH 1 108.230 376.560 ; O2 P O2 1 119.900 1171.520 ; O2 P OS 1 108.230 836.800 ; OH P OS 1 102.600 376.560 ; OS P OS 1 102.600 376.560 ; CT S CT 1 98.900 518.816 ; AA met CT S S 1 103.700 569.024 ; AA cyx (SCHERAGA JPC 79,1428) CT SH HS 1 96.000 359.824 ; changed from 44.0 based on methanethiol nmodes HS SH HS 1 92.070 292.880 ; AA cys F CT F 1 109.100 644.336 ; JCC,13,(1992),963; F CT H1 1 109.500 418.400 ; new99 N C N 1 120.000 585.760 ; Added for Urea (same as N2-CA-N2) - EJS [ dihedraltypes ] ;i j k l func phase kd pn ;impropers treated as propers in GROMACS to use correct AMBER analytical function CA CA CA OH 1 180.00 4.60240 2 ; new99 H5 O C OH 1 180.00 4.60240 2 ; new99 H5 O C OS 1 180.00 4.60240 2 ; new99 CM CT CM HA 1 180.00 4.60240 2 ; new99 CA CA CA Br 1 180.00 4.60240 2 ; new99 CM H4 C O 1 180.00 4.60240 2 ; new99 C CT N H 1 180.00 4.60240 2 ; new99 C CT N O 1 180.00 4.60240 2 ; new99 CK CB N* CT 1 180.00 4.18400 2 ; CM C N* CT 1 180.00 4.18400 2 ; dac guess, 9/94 CM C CM CT 1 180.00 4.60240 2 ; CT O C OH 1 180.00 43.93200 2 ; NA CV CC CT 1 180.00 4.60240 2 ; NB CW CC CT 1 180.00 4.60240 2 ; NA CW CC CT 1 180.00 4.60240 2 ; CW CB C* CT 1 180.00 4.60240 2 ; CA CA CA CT 1 180.00 4.60240 2 ; C CM CM CT 1 180.00 4.60240 2 ; dac guess, 9/94 NC CM CA N2 1 180.00 4.60240 2 ; dac guess, 9/94 CB NC CA N2 1 180.00 4.60240 2 ; dac, 10/94 NA NC CA N2 1 180.00 4.60240 2 ; dac, 10/94 CA CA C OH 1 180.00 4.60240 2 ; X O2 C O2 1 180.00 43.93200 2 ; JCC,7,(1986),230 X N2 CA N2 1 180.00 43.93200 2 ; JCC,7,(1986),230 X CT N CT 1 180.00 4.18400 2 ; JCC,7,(1986),230 X X C O 1 180.00 43.93200 2 ; JCC,7,(1986),230 X X N H 1 180.00 4.18400 2 ; JCC,7,(1986),230 X X N2 H 1 180.00 4.18400 2 ; JCC,7,(1986),230 X X NA H 1 180.00 4.18400 2 ; JCC,7,(1986),230 X X CA HA 1 180.00 4.60240 2 ; bsd.on C6H6 nmodes X X CW H4 1 180.00 4.60240 2 ; X X CR H5 1 180.00 4.60240 2 ; X X CV H4 1 180.00 4.60240 2 ; X X CQ H5 1 180.00 4.60240 2 ; X X CK H5 1 180.00 4.60240 2 ; X X CM H4 1 180.00 4.60240 2 ; X X CM HA 1 180.00 4.60240 2 ; X X CA H4 1 180.00 4.60240 2 ; bsd.on C6H6 nmodes X X CA H5 1 180.00 4.60240 2 ; bsd.on C6H6 nmodes #define urea_improper_1 180.00 43.93200 2 ; missing urea improper torsion around C #define nucleic_imp_10 180.00 4.18400 2 ; missing NA impropers due to defined propers #define nucleic_imp_11 180.00 4.60240 2 ; missing NA impropers due to defined propers [ dihedraltypes ] ;i j k l func C0 ... C5 ;propers treated as RBs in GROMACS to use combine multiple AMBER torsions per quartet CT CT OS CT 3 2.439272 4.807416 -0.836800 -6.409888 0.000000 0.000000 ; ; mainchain torsions changed in AMBER03 shown below ;N CT C N 3 23.84880 7.11280 -16.73600 0.00000 0.00000 0.00000 ; amber99 ;C N CT C 3 10.46000 -3.34720 -7.11280 0.00000 0.00000 0.00000 ; amber99 ;CT CT C N 3 0.83680 0.00000 -2.76144 0.00000 3.34720 0.00000 ; amber99 ;CT CT N C 3 2.84512 -4.10032 16.73600 2.51040 -16.73600 0.00000 ; amber99 N CT C N 3 16.95692 -2.93131 -12.16456 7.72366 0.00000 0.00000 ; amber03 C N CT C 3 8.08349 -1.41503 -2.88780 -3.78066 0.00000 0.00000 ; amber03 CT CT C N 3 4.04091 3.95974 -0.54978 -0.93722 0.00000 0.00000 ; amber03 C N CT CT 3 9.82361 -1.36942 -7.39396 3.79907 0.00000 0.00000 ; amber03 ; mainchain torsions changed in AMBER03 shown above ; additional 03GLY torsions below C N CT H0 3 12.42271 -1.91418 -10.50853 0.00000 0.00000 0.00000 ; amber03 GLY H0 CT C N 3 4.43797 4.43797 0.09205 0.00000 0.00000 0.00000 ; amber03 GLY ; additional 03GLY torsions above H N C O 3 29.28800 -8.36800 -20.92000 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 CT S S CT 3 2.51040 7.53120 29.28800 -10.04160 0.00000 0.00000 ; JCC,7,(1986),230 OS CT CT OS 3 0.60250 1.80749 9.83240 -2.40998 0.00000 0.00000 ; new99 OS CT CT OH 3 0.60250 1.80749 9.83240 -2.40998 0.00000 0.00000 ; new99 OH CT CT OH 3 0.60250 1.80749 9.83240 -2.40998 0.00000 0.00000 ; new99 OH P OS CT 3 1.04600 3.13800 10.04160 -4.18400 0.00000 0.00000 ; JCC,7,(1986),230 OS P OS CT 3 1.04600 3.13800 10.04160 -4.18400 0.00000 0.00000 ; JCC,7,(1986),230 OS CT N* CK 3 10.46000 -10.46000 0.00000 0.00000 0.00000 0.00000 ; new99 OS CT N* CM 3 10.46000 -10.46000 0.00000 0.00000 0.00000 0.00000 ; new99 H1 CT C O 3 3.68192 -4.35136 0.00000 1.33888 0.00000 0.00000 ; new99 - corrected below HC CT C O 3 3.68192 -4.35136 0.00000 1.33888 0.00000 0.00000 ; new99 - corrected below HC CT CT HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; new99 HC CT CT CT 3 0.66944 2.00832 0.00000 -2.67776 0.00000 0.00000 ; new99 HC CT CM CM 3 6.40152 -9.58136 0.00000 6.35968 0.00000 0.00000 ; new99 HO OH CT CT 3 1.71544 0.96232 0.00000 -2.67776 0.00000 0.00000 ; new99 HO OH C O 3 27.19600 -7.94960 -19.24640 0.00000 0.00000 0.00000 ; new99 CM CM C O 3 19.45560 3.76560 -18.20040 -5.02080 0.00000 0.00000 ; new99 CT CM CM CT 3 63.59680 7.94960 -55.64720 0.00000 0.00000 0.00000 ; new99 CT CT CT CT 3 3.68192 3.09616 -2.09200 -3.01248 0.00000 0.00000 ; new99 CT CT OS C 3 4.94967 8.15462 0.00000 -6.40989 0.00000 0.00000 ; new99 CT OS CT OS 3 13.17960 6.90360 -7.11280 -1.67360 0.00000 0.00000 ; new99 O C OS CT 3 28.45120 5.85760 -22.59360 0.00000 0.00000 0.00000 ; new99 F CT CT F 3 5.02080 5.02080 0.00000 0.00000 0.00000 0.00000 ; new99 Cl CT CT Cl 3 1.88280 1.88280 0.00000 0.00000 0.00000 0.00000 ; new99 Br CT CT Br 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; new99 H1 CT CT OS 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; new99 H1 CT CT OH 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; new99 H1 CT CT F 3 0.79496 -0.79496 0.00000 0.00000 0.00000 0.00000 ; new99 H1 CT CT Cl 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; new99 H1 CT CT Br 3 2.30120 -2.30120 0.00000 0.00000 0.00000 0.00000 ; new99 HC CT CT OS 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; new99 HC CT CT OH 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; new99 HC CT CT F 3 0.79496 -0.79496 0.00000 0.00000 0.00000 0.00000 ; new99 HC CT CT Cl 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; new99 HC CT CT Br 3 2.30120 -2.30120 0.00000 0.00000 0.00000 0.00000 ; new99 CT OS CT N* 3 1.60247 4.80742 5.43920 -6.40989 0.00000 0.00000 ; new99 X C C X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; new99 X C O X 3 23.43040 0.00000 -23.43040 0.00000 0.00000 0.00000 ; new99 X C OS X 3 22.59360 0.00000 -22.59360 0.00000 0.00000 0.00000 ; new99 X CA OH X 3 7.53120 0.00000 -7.53120 0.00000 0.00000 0.00000 ; new99 X CM OS X 3 8.78640 0.00000 -8.78640 0.00000 0.00000 0.00000 ; new99 X C CA X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; intrpol.bsd.on C6H6 X C CB X 3 25.10400 0.00000 -25.10400 0.00000 0.00000 0.00000 ; intrpol.bsd.on C6H6 X C CM X 3 18.20040 0.00000 -18.20040 0.00000 0.00000 0.00000 ; intrpol.bsd.on C6H6 X C N* X 3 12.13360 0.00000 -12.13360 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X C NA X 3 11.29680 0.00000 -11.29680 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X C NC X 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X C OH X 3 19.24640 0.00000 -19.24640 0.00000 0.00000 0.00000 ; new99 X C CT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CA CA X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; intrpol.bsd.on C6H6 X CA CB X 3 29.28800 0.00000 -29.28800 0.00000 0.00000 0.00000 ; intrpol.bsd.on C6H6 X CA CM X 3 21.33840 0.00000 -21.33840 0.00000 0.00000 0.00000 ; intrpol.bsd.on C6H6 X CA CT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CA N2 X 3 20.08320 0.00000 -20.08320 0.00000 0.00000 0.00000 ; reinterpolated 93' X CA NA X 3 12.55200 0.00000 -12.55200 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CA NC X 3 40.16640 0.00000 -40.16640 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CB CB X 3 45.60560 0.00000 -45.60560 0.00000 0.00000 0.00000 ; intrpol.bsd.on C6H6 X CB N* X 3 13.80720 0.00000 -13.80720 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CB NB X 3 21.33840 0.00000 -21.33840 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CB NC X 3 34.72720 0.00000 -34.72720 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CK N* X 3 14.22560 0.00000 -14.22560 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CK NB X 3 83.68000 0.00000 -83.68000 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CM CM X 3 55.64720 0.00000 -55.64720 0.00000 0.00000 0.00000 ; intrpol.bsd.on C6H6 X CM CT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CM N* X 3 15.48080 0.00000 -15.48080 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CQ NC X 3 56.90240 0.00000 -56.90240 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CT CT X 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; JCC,7,(1986),230 X CT N X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CT N* X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CT N2 X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CT OH X 3 0.69733 2.09200 0.00000 -2.78933 0.00000 0.00000 ; JCC,7,(1986),230 X CT OS X 3 1.60387 4.81160 0.00000 -6.41547 0.00000 0.00000 ; JCC,7,(1986),230 X OH P X 3 1.04600 3.13800 0.00000 -4.18400 0.00000 0.00000 ; JCC,7,(1986),230 X OS P X 3 1.04600 3.13800 0.00000 -4.18400 0.00000 0.00000 ; JCC,7,(1986),230 X C N X 3 20.92000 0.00000 -20.92000 0.00000 0.00000 0.00000 ; AA|check Wendy?&NMA X CT N3 X 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; JCC,7,(1986),230 X CT S X 3 1.39467 4.18400 0.00000 -5.57867 0.00000 0.00000 ; JCC,7,(1986),230 X CT SH X 3 1.04600 3.13800 0.00000 -4.18400 0.00000 0.00000 ; JCC,7,(1986),230 X C* CB X 3 14.01640 0.00000 -14.01640 0.00000 0.00000 0.00000 ; intrpol.bsd.onC6H6aa X C* CT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X C* CW X 3 54.60120 0.00000 -54.60120 0.00000 0.00000 0.00000 ; intrpol.bsd.on C6H6 X CA CN X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; reinterpolated 93' X CB CN X 3 25.10400 0.00000 -25.10400 0.00000 0.00000 0.00000 ; reinterpolated 93' X CC CT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CC CV X 3 43.09520 0.00000 -43.09520 0.00000 0.00000 0.00000 ; intrpol.bsd.on C6H6 X CC CW X 3 44.97800 0.00000 -44.97800 0.00000 0.00000 0.00000 ; intrpol.bsd.on C6H6 X CC NA X 3 11.71520 0.00000 -11.71520 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CC NB X 3 20.08320 0.00000 -20.08320 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CN NA X 3 12.76120 0.00000 -12.76120 0.00000 0.00000 0.00000 ; reinterpolated 93' X CR NA X 3 19.45560 0.00000 -19.45560 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CR NB X 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CV NB X 3 20.08320 0.00000 -20.08320 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 X CW NA X 3 12.55200 0.00000 -12.55200 0.00000 0.00000 0.00000 ; JCC,7,(1986),230 ; missing protein mainchain torsions #define backbone_prop_1 20.92000 0.00000 -20.92000 0.00000 0.00000 0.00000 ; CT-C-N-H #define backbone_prop_2 29.28800 -8.36800 -20.92000 0.00000 0.00000 0.00000 ; O-C-N-H ;#define backbone_prop_3 2.84512 -4.10032 16.73600 2.51040 -16.73600 0.00000 ; old amber99 #define backbone_prop_3 9.82361 -1.36942 -7.39396 3.79907 0.00000 0.00000 ; new amber03 C-N-CT-Cb ;#define backbone_prop_4 10.46000 -3.34720 -7.11280 0.00000 0.00000 0.00000 ; old amber99 #define backbone_prop_4 8.08349 -1.41503 -2.88780 -3.78066 0.00000 0.00000 ; new amber03 C-N-CT-C #define backbone_prop_5 12.42271 -1.91418 -10.50853 0.00000 0.00000 0.00000 ; new 03GLY C-N-CT-H0 #define backbone_prop_6 4.43797 4.43797 0.09205 0.00000 0.00000 0.00000 ; new 03GLY H0-CT-C-N ; missing protein sidechain torsions #define sidechain_prop_1 20.08320 0.00000 -20.08320 0.00000 0.00000 0.00000 ; ARG sidechains ;#define proline_prop_1 2.84512 -4.10032 16.73600 2.51040 -16.73600 0.00000 ; old amber99 torsion #define proline_prop_1 9.82361 -1.36942 -7.39396 3.79907 0.00000 0.00000 ; new amber03 torsion #define hyp_prop_1 0.65270 1.95811 12.46832 -2.61082 0.00000 0.00000 ; HYP for amber99: S Park, R J Radmer, T E Klein & V S Pande (submitted). #define aromatic_prop_1 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; X-CA-CA-X #define aromatic_prop_2 19.24640 0.00000 -19.24640 0.00000 0.00000 0.00000 ; X-C -OH-X (TYR) #define aromatic_prop_3 11.71520 0.00000 -11.71520 0.00000 0.00000 0.00000 ; X-CC-NA-X (HIX) #define aromatic_prop_3a 20.08320 0.00000 -20.08320 0.00000 0.00000 0.00000 ; X-CC-NB-X (HIX) #define aromatic_prop_4 12.55200 0.00000 -12.55200 0.00000 0.00000 0.00000 ; X-CW-NA-X (HIX) #define aromatic_prop_4a 20.08320 0.00000 -20.08320 0.00000 0.00000 0.00000 ; X-CV-NB-X (HIX) #define aromatic_prop_5 19.45560 0.00000 -19.45560 0.00000 0.00000 0.00000 ; X-CR-NA-X (HIX) #define aromatic_prop_5a 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; X-CR-NB-X (HIX) #define aromatic_prop_6 44.97800 0.00000 -44.97800 0.00000 0.00000 0.00000 ; X-CC-CW-X (HIX) #define aromatic_prop_6a 43.09520 0.00000 -43.09520 0.00000 0.00000 0.00000 ; X-CC-CV-X (HIX) #define aromatic_prop_7 54.60120 0.00000 -54.60120 0.00000 0.00000 0.00000 ; X-C*-CW-X (TRP) #define aromatic_prop_8 14.01640 0.00000 -14.01640 0.00000 0.00000 0.00000 ; X-C*-CB-X (TRP) #define aromatic_prop_9 12.76120 0.00000 -12.76120 0.00000 0.00000 0.00000 ; X-NA-CN-X (TRP) #define aromatic_prop_10 25.10400 0.00000 -25.10400 0.00000 0.00000 0.00000 ; X-CN-CB-X (TRP) #define aromatic_prop_11 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; X-CN-CA-X (TRP) #define aromatic_prop_12 29.28800 0.00000 -29.28800 0.00000 0.00000 0.00000 ; X-CB-CA-X (TRP) ; missing nucleic torsions #define proper_X_CT_N*_X 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 #define proper_X_CM_CT_X 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 #define proper_X_CK_N*_X 14.22560 0.00000 -14.22560 0.00000 0.00000 0.00000 #define proper_X_CB_N*_X 13.80720 0.00000 -13.80720 0.00000 0.00000 0.00000 #define proper_X_CA_NC_X 40.16640 0.00000 -40.16640 0.00000 0.00000 0.00000 #define proper_X_CQ_NC_X 56.90240 0.00000 -56.90240 0.00000 0.00000 0.00000 #define proper_X_C_N*_X 12.13360 0.00000 -12.13360 0.00000 0.00000 0.00000 #define proper_X_CM_CM_X 55.64720 0.00000 -55.64720 0.00000 0.00000 0.00000 #define proper_X_C_NC_X 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 #define proper_X_CA_CM_X 21.33840 0.00000 -21.33840 0.00000 0.00000 0.00000 #define proper_X_C_NA_X 11.29680 0.00000 -11.29680 0.00000 0.00000 0.00000 #define proper_X_CA_NA_X 12.55200 0.00000 -12.55200 0.00000 0.00000 0.00000 #define proper_X_CK_NB_X 83.68000 0.00000 -83.68000 0.00000 0.00000 0.00000 #define proper_X_C_CM_X 18.20040 0.00000 -18.20040 0.00000 0.00000 0.00000 #define proper_CM_CM_C_O 19.45560 3.76560 -18.20040 -5.02080 0.00000 0.00000 #define proper_HC_CT_CM_CM 6.40152 -9.58136 0.00000 6.35968 0.00000 0.00000 #define proper_X_CA_N2_X 20.08320 0.00000 -20.08320 0.00000 0.00000 0.00000 #define proper_X_N*_CM_X 15.48080 0.00000 -15.48080 0.00000 0.00000 0.00000 #define proper_H_CT_CT_O 1.696840 0.90653 0.00000 -2.60338 0.00000 0.00000