--- /dev/null
+[ bondtypes ]
+; i j func b0 kb
+ 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
+;
+; New atomtype for C5' in DNA/RNA (checked with conversion and is the same as CT)
+;
+ CI H1 1 0.10900 284512.0
+ CI CT 1 0.15260 259408.0
+ CI OH 1 0.14100 267776.0
+ CI OS 1 0.14100 267776.0
+
+
+[ constrainttypes ]
+; this section is implemented manually from bond & angle values
+
+; constraints for rigid CH3 groups
+ MCH3 CT 2 0.166426
+ MCH3 S 2 0.193875
+ MCH3 MCH3 2 0.092163
+; constraints for rigid NH3 groups
+ MNH3 CT 2 0.158254
+ MNH3 MNH3 2 0.080229
+
+; angle-derived constraints for OH and SH groups in proteins
+; The constraint A-C is calculated from the angle A-B-C and bonds A-B, B-C.
+ C HO 2 0.195074
+ CA HO 2 0.195074
+ CT HO 2 0.194132
+ CT HS 2 0.235935
+
+
+
+[ angletypes ]
+; i j k func th0 cth
+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
+;
+; New atomtype for C5' in DNA/RNA (checked with conversion and is the same as CT)
+;
+CT CI H1 1 109.500 418.400
+H1 CI H1 1 109.500 292.880
+CI CT H1 1 109.500 418.400
+CI CT OS 1 109.500 418.400
+CI CT CT 1 109.500 334.720
+H1 CI OS 1 109.500 418.400
+CT CI OS 1 109.500 418.400
+CI OS P 1 120.500 836.800
+H1 CI OH 1 109.500 418.400
+CT CI OH 1 109.500 418.400
+CI OH HO 1 108.500 460.240
+
+[ dihedraltypes ]
+;i j k l func phase kd pn
+CA CA CA OH 4 180.00 4.60240 2 ; new99
+H5 O C OH 4 180.00 4.60240 2 ; new99
+H5 O C OS 4 180.00 4.60240 2 ; new99
+CM CT CM HA 4 180.00 4.60240 2 ; new99
+CA CA CA Br 4 180.00 4.60240 2 ; new99
+CM H4 C O 4 180.00 4.60240 2 ; new99
+C CT N H 4 180.00 4.60240 2 ; new99
+C CT N O 4 180.00 4.60240 2 ; new99
+CB CK N* CT 4 180.00 4.18400 2 ;
+CK CB N* CT 4 180.00 4.18400 2 ;
+C CM N* CT 4 180.00 4.18400 2 ; dac guess, 9/94
+CT N* C CM 4 180.00 4.18400 2 ;
+CM C CM CT 4 180.00 4.60240 2 ;
+CT O C OH 4 180.00 43.93200 2 ;
+NA CV CC CT 4 180.00 4.60240 2 ;
+NB CW CC CT 4 180.00 4.60240 2 ;
+NA CW CC CT 4 180.00 4.60240 2 ;
+CW CB C* CT 4 180.00 4.60240 2 ;
+CA CA CA CT 4 180.00 4.60240 2 ;
+C CM CM CT 4 180.00 4.60240 2 ; dac guess, 9/94
+NC CM CA N2 4 180.00 4.60240 2 ; dac guess, 9/94
+CB NC CA N2 4 180.00 4.60240 2 ; dac, 10/94
+NA NC CA N2 4 180.00 4.60240 2 ; dac, 10/94
+CA CA C OH 4 180.00 4.60240 2 ;
+CT CV CC NA 4 180.00 4.60240 2 ;
+CT CW CC NB 4 180.00 4.60240 2 ;
+CT CW CC NA 4 180.00 4.60240 2 ;
+CB CT C* CW 4 180.00 4.60240 2 ;
+CM N2 CA NC 4 180.00 4.60240 2 ;
+CB N2 CA NC 4 180.00 4.60240 2 ;
+N2 NA CA NC 4 180.00 4.60240 2 ;
+N N C O 4 180.00 43.93200 2 ; urea
+X O2 C O2 4 180.00 43.93200 2 ; JCC,7,(1986),230
+X N2 CA N2 4 180.00 43.93200 2 ; JCC,7,(1986),230
+X CT N CT 4 180.00 4.18400 2 ; JCC,7,(1986),230
+X X C O 4 180.00 43.93200 2 ; JCC,7,(1986),230
+X X N H 4 180.00 4.18400 2 ; JCC,7,(1986),230
+X X N2 H 4 180.00 4.18400 2 ; JCC,7,(1986),230
+X X NA H 4 180.00 4.18400 2 ; JCC,7,(1986),230
+X X CA HA 4 180.00 4.60240 2 ; bsd.on C6H6 nmodes
+X X CW H4 4 180.00 4.60240 2 ;
+X X CR H5 4 180.00 4.60240 2 ;
+X X CV H4 4 180.00 4.60240 2 ;
+X X CQ H5 4 180.00 4.60240 2 ;
+X X CK H5 4 180.00 4.60240 2 ;
+X X CM H4 4 180.00 4.60240 2 ;
+X X CM HA 4 180.00 4.60240 2 ;
+X X CA H4 4 180.00 4.60240 2 ; bsd.on C6H6 nmodes
+X X CA H5 4 180.00 4.60240 2 ; bsd.on C6H6 nmodes
+
+
+[ dihedraltypes ]
+;i j k l func
+;
+; New dihedrals for C5' in DNA/RNA
+;
+ CT OS CT CI 9 0.0 1.60247 3
+ CT OS CT CI 9 180.0 0.41840 2
+ H1 CI CT OS 9 0.0 1.04600 1
+ H1 CI CT OH 9 0.0 1.04600 1
+ H1 CT CI OS 9 0.0 1.04600 1
+ H1 CT CI OH 9 0.0 1.04600 1
+ CI CT CT CT 9 0.0 0.75312 3
+ CI CT CT CT 9 180.0 1.04600 2
+ CI CT CT CT 9 180.0 0.83680 1
+;
+ OS P OS CI 9 31.795 0.774797 1 ; alpha (6DP after conversion, as 6DP given in paper)
+ OS P OS CI 9 351.9596 5.257326 2 ; alpha
+ OS P OS CI 9 357.24748 1.484726 3 ; alpha
+ OH P OS CI 9 31.795 0.774797 1 ; alpha
+ OH P OS CI 9 351.9596 5.257326 2 ; alpha
+ OH P OS CI 9 357.24748 1.484726 3 ; alpha
+ CT CT CI OS 9 190.97653 4.928919 1 ; gamma
+ CT CT CI OS 9 295.63279 0.385355 2 ; gamma
+ CT CT CI OS 9 348.09535 4.028481 3 ; gamma
+ CT CT CI OH 9 190.97653 4.928919 1 ; gamma
+ CT CT CI OH 9 295.63279 0.385355 2 ; gamma
+ CT CT CI OH 9 348.09535 4.028481 3 ; gamma
+;
+ X CI OS X 9 0.0 1.60387 3
+ X CI OH X 9 0.0 0.69733 3
+ X CI CT X 9 0.0 0.65084 3
+;
+; Back to normal dihedrals
+;
+ CT CT OS CT 9 0.0 1.60247 3 ;
+ CT CT OS CT 9 180.0 0.41840 2 ;
+ C N CT C 9 0.0 1.12968 2 ; new for 99sb
+ C N CT C 9 0.0 1.75728 3 ; new for 99sb
+ N CT C N 9 180.0 1.88280 1 ; new for 99sb
+ N CT C N 9 180.0 6.61072 2 ; new for 99sb
+ N CT C N 9 180.0 2.30120 3 ; new for 99sb
+ CT CT N C 9 0.0 8.36800 1 ; new for 99sb
+ CT CT N C 9 0.0 8.36800 2 ; new for 99sb
+ CT CT N C 9 0.0 1.67360 3 ; new for 99sb
+ CT CT C N 9 0.0 0.83680 1 ; new for 99sb
+ CT CT C N 9 0.0 0.83680 2 ; new for 99sb
+ CT CT C N 9 0.0 1.67360 3 ; new for 99sb
+ H N C O 9 180.0 10.46000 2 ; JCC,7,(1986),230
+ H N C O 9 0.0 8.36800 1 ; J.C.cistrans-NMA DE
+ CT S S CT 9 0.0 14.64400 2 ; JCC,7,(1986),230
+ CT S S CT 9 0.0 2.51040 3 ; JCC,7,(1986),230
+ OS CT CT OS 9 0.0 0.60250 3 ; parm98, TC,PC,PAK
+ OS CT CT OS 9 0.0 4.91620 2 ; Piotr et al.
+ OS CT CT OH 9 0.0 0.60250 3 ; parm98, TC,PC,PAK
+ OS CT CT OH 9 0.0 4.91620 2 ; parm98, TC,PC,PAK
+ OH CT CT OH 9 0.0 0.60250 3 ; parm98, TC,PC,PAK
+ OH CT CT OH 9 0.0 4.91620 2 ; parm98, TC,PC,PAK
+ OH P OS CT 9 0.0 1.04600 3 ; JCC,7,(1986),230
+ OH P OS CT 9 0.0 5.02080 2 ; gg> ene.631g*/mp2
+ OS P OS CT 9 0.0 1.04600 3 ; JCC,7,(1986),230
+ OS P OS CT 9 0.0 5.02080 2 ; gg> ene.631g*/mp2
+ OS CT N* CK 9 0.0 10.46000 1 ; parm98, TC,PC,PAK
+ OS CT N* CM 9 0.0 10.46000 1 ; parm98, TC,PC,PAK
+ H1 CT C O 9 0.0 3.34720 1 ; Junmei et al, 1999
+ H1 CT C O 9 180.0 0.33472 3 ; Junmei et al, 1999
+ HC CT C O 9 0.0 3.34720 1 ; Junmei et al, 1999
+ HC CT C O 9 180.0 0.33472 3 ; Junmei et al, 1999
+ HC CT CT HC 9 0.0 0.62760 3 ; Junmei et al, 1999
+ HC CT CT CT 9 0.0 0.66944 3 ; Junmei et al, 1999
+ HC CT CM CM 9 180.0 1.58992 3 ; Junmei et al, 1999
+ HC CT CM CM 9 0.0 4.81160 1 ; Junmei et al, 1999
+ HO OH CT CT 9 0.0 0.66944 3 ; Junmei et al, 1999
+ HO OH CT CT 9 0.0 1.04600 1 ; Junmei et al, 1999
+ HO OH C O 9 180.0 9.62320 2 ; Junmei et al, 1999
+ HO OH C O 9 0.0 7.94960 1 ; Junmei et al, 1999
+ CM CM C O 9 180.0 9.10020 2 ; Junmei et al, 1999
+ CM CM C O 9 0.0 1.25520 3 ; Junmei et al, 1999
+ CT CM CM CT 9 180.0 27.82360 2 ; Junmei et al, 1999
+ CT CM CM CT 9 180.0 7.94960 1 ; Junmei et al, 1999
+ CT CT CT CT 9 0.0 0.75312 3 ; Junmei et al, 1999
+ CT CT CT CT 9 180.0 1.04600 2 ; Junmei et al, 1999
+ CT CT CT CT 9 180.0 0.83680 1 ; Junmei et al, 1999
+ CT CT OS C 9 0.0 1.60247 3 ; Junmei et al, 1999
+ CT CT OS C 9 180.0 3.34720 1 ; Junmei et al, 1999
+ CT OS CT OS 9 0.0 0.41840 3 ; Junmei et al, 1999
+ CT OS CT OS 9 180.0 3.55640 2 ; Junmei et al, 1999
+ CT OS CT OS 9 180.0 5.64840 1 ; Junmei et al, 1999
+ O C OS CT 9 180.0 11.29680 2 ; Junmei et al, 1999
+ O C OS CT 9 180.0 5.85760 1 ; Junmei et al, 1999
+ F CT CT F 9 180.0 5.02080 1 ; Junmei et al, 1999
+ Cl CT CT Cl 9 180.0 1.88280 1 ; Junmei et al, 1999
+ Br CT CT Br 9 0.0 0.00000 0 ; Junmei et al, 1999
+ H1 CT CT OS 9 0.0 1.04600 1 ; Junmei et al, 1999
+ H1 CT CT OH 9 0.0 1.04600 1 ; Junmei et al, 1999
+ H1 CT CT F 9 0.0 0.79496 1 ; Junmei et al, 1999
+ H1 CT CT Cl 9 0.0 1.04600 1 ; Junmei et al, 1999
+ H1 CT CT Br 9 0.0 2.30120 1 ; Junmei et al, 1999
+ HC CT CT OS 9 0.0 1.04600 1 ; Junmei et al, 1999
+ HC CT CT OH 9 0.0 1.04600 1 ; Junmei et al, 1999
+ HC CT CT F 9 0.0 0.79496 1 ; Junmei et al, 1999
+ HC CT CT Cl 9 0.0 1.04600 1 ; Junmei et al, 1999
+ HC CT CT Br 9 0.0 2.30120 1 ; Junmei et al, 1999
+ CT OS CT N* 9 0.0 1.60247 3 ; parm98.dat, TC,PC,PAK
+ CT OS CT N* 9 0.0 2.71960 2 ; Piotr et al.
+ X C C X 9 180.0 15.16700 2 ; Junmei et al, 1999
+ X C O X 9 180.0 11.71520 2 ; Junmei et al, 1999
+ X C OS X 9 180.0 11.29680 2 ; Junmei et al, 1999
+ X CA OH X 9 180.0 3.76560 2 ; Junmei et al, 99
+ X CM OS X 9 180.0 4.39320 2 ; Junmei et al, 1999
+ X C CA X 9 180.0 15.16700 2 ; intrpol.bsd.on C6H6
+ X C CB X 9 180.0 12.55200 2 ; intrpol.bsd.on C6H6
+ X C CM X 9 180.0 9.10020 2 ; intrpol.bsd.on C6H6
+ X C N* X 9 180.0 6.06680 2 ; JCC,7,(1986),230
+ X C NA X 9 180.0 5.64840 2 ; JCC,7,(1986),230
+ X C NC X 9 180.0 16.73600 2 ; JCC,7,(1986),230
+ X C OH X 9 180.0 9.62320 2 ; Junmei et al, 1999
+ X C CT X 9 0.0 0.00000 0 ; JCC,7,(1986),230
+ X CA CA X 9 180.0 15.16700 2 ; intrpol.bsd.on C6H6
+ X CA CB X 9 180.0 14.64400 2 ; intrpol.bsd.on C6H6
+ X CA CM X 9 180.0 10.66920 2 ; intrpol.bsd.on C6H6
+ X CA CT X 9 0.0 0.00000 0 ; JCC,7,(1986),230
+ X CA N2 X 9 180.0 10.04160 2 ; reinterpolated 93'
+ X CA NA X 9 180.0 6.27600 2 ; JCC,7,(1986),230
+ X CA NC X 9 180.0 20.08320 2 ; JCC,7,(1986),230
+ X CB CB X 9 180.0 22.80280 2 ; intrpol.bsd.on C6H6
+ X CB N* X 9 180.0 6.90360 2 ; JCC,7,(1986),230
+ X CB NB X 9 180.0 10.66920 2 ; JCC,7,(1986),230
+ X CB NC X 9 180.0 17.36360 2 ; JCC,7,(1986),230
+ X CK N* X 9 180.0 7.11280 2 ; JCC,7,(1986),230
+ X CK NB X 9 180.0 41.84000 2 ; JCC,7,(1986),230
+ X CM CM X 9 180.0 27.82360 2 ; intrpol.bsd.on C6H6
+ X CM CT X 9 0.0 0.00000 0 ; JCC,7,(1986),230
+ X CM N* X 9 180.0 7.74040 2 ; JCC,7,(1986),230
+ X CQ NC X 9 180.0 28.45120 2 ; JCC,7,(1986),230
+ X CT CT X 9 0.0 0.65084 3 ; JCC,7,(1986),230
+ X CT N X 9 0.0 0.00000 0 ; JCC,7,(1986),230
+ X CT N* X 9 0.0 0.00000 0 ; JCC,7,(1986),230
+ X CT N2 X 9 0.0 0.00000 0 ; JCC,7,(1986),230
+ X CT OH X 9 0.0 0.69733 3 ; JCC,7,(1986),230
+ X CT OS X 9 0.0 1.60387 3 ; JCC,7,(1986),230
+ X OH P X 9 0.0 1.04600 3 ; JCC,7,(1986),230
+ X OS P X 9 0.0 1.04600 3 ; JCC,7,(1986),230
+ X C N X 9 180.0 10.46000 2 ; AA,NMA
+ X CT N3 X 9 0.0 0.65084 3 ; JCC,7,(1986),230
+ X CT S X 9 0.0 1.39467 3 ; JCC,7,(1986),230
+ X CT SH X 9 0.0 1.04600 3 ; JCC,7,(1986),230
+ X C* CB X 9 180.0 7.00820 2 ; intrpol.bsd.onC6H6aa
+ X C* CT X 9 0.0 0.00000 0 ; JCC,7,(1986),230
+ X C* CW X 9 180.0 27.30060 2 ; intrpol.bsd.on C6H6
+ X CA CN X 9 180.0 15.16700 2 ; reinterpolated 93'
+ X CB CN X 9 180.0 12.55200 2 ; reinterpolated 93'
+ X CC CT X 9 0.0 0.00000 0 ; JCC,7,(1986),230
+ X CC CV X 9 180.0 21.54760 2 ; intrpol.bsd.on C6H6
+ X CC CW X 9 180.0 22.48900 2 ; intrpol.bsd.on C6H6
+ X CC NA X 9 180.0 5.85760 2 ; JCC,7,(1986),230
+ X CC NB X 9 180.0 10.04160 2 ; JCC,7,(1986),230
+ X CN NA X 9 180.0 6.38060 2 ; reinterpolated 93'
+ X CR NA X 9 180.0 9.72780 2 ; JCC,7,(1986),230
+ X CR NB X 9 180.0 20.92000 2 ; JCC,7,(1986),230
+ X CV NB X 9 180.0 10.04160 2 ; JCC,7,(1986),230
+ X CW NA X 9 180.0 6.27600 2 ; JCC,7,(1986),230
+; Modified amino acid torsions in Amber99SB-ILDN
+; These should not override the general torsion for the atom types,
+; so to avoid introducing extra new atom types we list them explicitly for
+; the residues in question:
+
+#define torsion_ILE_N_CA_CB_CG2_mult1 0.0 0.8158800 1 ; Proteins 78, 1950 (2010)
+#define torsion_ILE_N_CA_CB_CG2_mult2 0.0 -3.5396640 2 ; Proteins 78, 1950 (2010)
+
+#define torsion_LEU_C_CA_CB_CG_mult1 0.0 2.3890640 1 ; Proteins 78, 1950 (2010)
+#define torsion_LEU_C_CA_CB_CG_mult2 0.0 -1.4978720 2 ; Proteins 78, 1950 (2010)
+#define torsion_LEU_C_CA_CB_CG_mult3 0.0 0.5648400 3 ; Proteins 78, 1950 (2010)
+
+#define torsion_ASP_N_CA_CB_CG_mult1 0.0 -11.024840 1 ; Proteins 78, 1950 (2010)
+#define torsion_ASP_N_CA_CB_CG_mult2 0.0 -4.978960 2 ; Proteins 78, 1950 (2010)
+#define torsion_ASP_N_CA_CB_CG_mult3 0.0 -0.029288 3 ; Proteins 78, 1950 (2010)
+#define torsion_ASP_N_CA_CB_CG_mult4 0.0 1.769832 4 ; Proteins 78, 1950 (2010)
+#define torsion_ASP_N_CA_CB_CG_mult5 0.0 0.970688 5 ; Proteins 78, 1950 (2010)
+#define torsion_ASP_N_CA_CB_CG_mult6 0.0 -0.891192 6 ; Proteins 78, 1950 (2010)
+
+#define torsion_ASP_CA_CB_CG_OD_mult1 0.0 0.0 1 ; Proteins 78, 1950 (2010)
+#define torsion_ASP_CA_CB_CG_OD_mult2 0.0 -1.853512 2 ; Proteins 78, 1950 (2010)
+#define torsion_ASP_CA_CB_CG_OD_mult3 0.0 0.0 3 ; Proteins 78, 1950 (2010)
+#define torsion_ASP_CA_CB_CG_OD_mult4 0.0 -0.577392 4 ; Proteins 78, 1950 (2010)
+#define torsion_ASP_CA_CB_CG_OD_mult5 0.0 0.0 5 ; Proteins 78, 1950 (2010)
+#define torsion_ASP_CA_CB_CG_OD_mult6 0.0 -0.054392 6 ; Proteins 78, 1950 (2010)
+
+#define torsion_ASN_C_CA_CB_CG_mult1 0.0 2.389064 1 ; Proteins 78, 1950 (2010)
+#define torsion_ASN_C_CA_CB_CG_mult2 0.0 -2.493664 2 ; Proteins 78, 1950 (2010)
+#define torsion_ASN_C_CA_CB_CG_mult3 0.0 0.493712 3 ; Proteins 78, 1950 (2010)
+#define torsion_ASN_C_CA_CB_CG_mult4 0.0 -1.744728 4 ; Proteins 78, 1950 (2010)
+#define torsion_ASN_C_CA_CB_CG_mult5 0.0 0.435136 5 ; Proteins 78, 1950 (2010)
+#define torsion_ASN_C_CA_CB_CG_mult6 0.0 -0.422584 6 ; Proteins 78, 1950 (2010)
+
+#define torsion_ASN_CA_CB_CG_ND2_mult1 0.0 -4.376464 1 ; Proteins 78, 1950 (2010)
+#define torsion_ASN_CA_CB_CG_ND2_mult2 0.0 -0.757304 2 ; Proteins 78, 1950 (2010)
+#define torsion_ASN_CA_CB_CG_ND2_mult3 0.0 -0.146440 3 ; Proteins 78, 1950 (2010)
+#define torsion_ASN_CA_CB_CG_ND2_mult4 0.0 0.418400 4 ; Proteins 78, 1950 (2010)
+#define torsion_ASN_CA_CB_CG_ND2_mult5 0.0 0.543920 5 ; Proteins 78, 1950 (2010)
+#define torsion_ASN_CA_CB_CG_ND2_mult6 0.0 -0.443504 6 ; Proteins 78, 1950 (2010)
+
+
+
+
+