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|
; ########################################################################
; # #
; # 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
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