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Copy pathSRP-RNA_BzCN_GMX-proc.top
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SRP-RNA_BzCN_GMX-proc.top
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; Include forcefield parameters
********************************************************************
* The original ffamber ports were written by Eric J. Sorin, *
* CSU Long Beach, Dept. of Chem & Biochem, and have now been *
* integrated with the standard gromacs distribution. *
* (Please don't blame Eric for errors we might have introduced.) *
* For the implementation/validation, please read/cite: *
* Sorin & Pande (2005). Biophys. J. 88(4), 2472-2493. *
* For related material and updates, please consult *
* http://chemistry.csulb.edu/ffamber/ *
********************************************************************
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333
[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
C 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CA 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CB 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CC 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CK 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CM 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CN 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CQ 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CR 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CT 6 12.01 0.0000 A 3.39967e-01 4.57730e-01
CV 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CW 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
C* 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CY 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 ; shape reagent; nitrile C (Howard et al.JCC,16,243,1995)
C0 20 40.08 0.0000 A 3.05240e-01 1.92376e+00
H 1 1.008 0.0000 A 1.06908e-01 6.56888e-02
HC 1 1.008 0.0000 A 2.64953e-01 6.56888e-02
H1 1 1.008 0.0000 A 2.47135e-01 6.56888e-02
H2 1 1.008 0.0000 A 2.29317e-01 6.56888e-02
H3 1 1.008 0.0000 A 2.11499e-01 6.56888e-02
HA 1 1.008 0.0000 A 2.59964e-01 6.27600e-02
H4 1 1.008 0.0000 A 2.51055e-01 6.27600e-02
H5 1 1.008 0.0000 A 2.42146e-01 6.27600e-02
HO 1 1.008 0.0000 A 0.00000e+00 0.00000e+00
HS 1 1.008 0.0000 A 1.06908e-01 6.56888e-02
HW 1 1.008 0.0000 A 0.00000e+00 0.00000e+00
HP 1 1.008 0.0000 A 1.95998e-01 6.56888e-02
IB 0 131.0 0.0000 A 8.90899e-01 4.18400e-01
N 7 14.01 0.0000 A 3.25000e-01 7.11280e-01
NA 7 14.01 0.0000 A 3.25000e-01 7.11280e-01
NB 7 14.01 0.0000 A 3.25000e-01 7.11280e-01
NC 7 14.01 0.0000 A 3.25000e-01 7.11280e-01
N2 7 14.01 0.0000 A 3.25000e-01 7.11280e-01
N3 7 14.01 0.0000 A 3.25000e-01 7.11280e-01
N* 7 14.01 0.0000 A 3.25000e-01 7.11280e-01
NY 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 ; shape reagent; nitrile N (Howard et al.JCC,16,243,1995)
NO 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 ; shape reagent; Nitro N (gaff2, Version 2.1, April 2016)
O 8 16.00 0.0000 A 2.95992e-01 8.78640e-01
OW 8 16.00 0.0000 A 3.15061e-01 6.36386e-01
OH 8 16.00 0.0000 A 3.06647e-01 8.80314e-01
OS 8 16.00 0.0000 A 3.00001e-01 7.11280e-01
O2 8 16.00 0.0000 A 2.95992e-01 8.78640e-01
P 15 30.97 0.0000 A 3.74177e-01 8.36800e-01
S 16 32.06 0.0000 A 3.56359e-01 1.04600e+00
SH 16 32.06 0.0000 A 3.56359e-01 1.04600e+00
CU 29 63.55 0.0000 A 3.39967e-01 3.59824e-01
FE 26 55.00 0.0000 A 0.00000e+00 0.00000e+00
; spc water - use only with spc.itp & settles
OW_spc 8 15.9994 0.0000 A 3.16557e-01 6.50629e-01
HW_spc 1 1.0080 0.0000 A 0.00000e+00 0.00000e+00
Zn 30 65.4 0.0000 A 1.95998e-01 5.23000e-02
;tip4p-EW
HW_tip4pew 1 1.008 0.0000 A 0.00000e+00 0.00000e+00
OW_tip4pew 8 16.00 0.0000 A 3.16435e-01 6.80946e-01
; tip4p
HW_tip4p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00
OW_tip4p 8 16.00 0.0000 A 3.15365e-01 6.48520e-01
;tip5p
HW_tip5p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00
OW_tip5p 8 16.00 0.0000 A 3.12000e-01 6.69440e-01
; dummy defs
; MW=Dummy mass for tip4p/EW/5p water extra point charge
MW 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00
; Dummy masses for rigid CH3 and NH3 groups
MCH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00
MNH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00
;
;
CI 6 12.01 0.0000 A 3.39967e-01 4.57730e-01 ; New atomtype for C5' in DNA/RNA (parmbsc0
Br 35 79.90 0.0000 A 4.64693-01 2.45414e-01 ; corrected from Cheatham (old 0.00000e+00 0.00000e+00)
F 9 19.00 0.0000 A 4.10348e-01 1.40750e-02 ; corrected from Cheatham (old 3.11815e-01 2.55224e-01)
I 53 126.9 0.0000 A 5.09594e-01 2.24604e-01 ; corrected from Cheatham (old 4.18722e-01 1.67360e+00)
Cl 17 35.45 0.0000 A 4.47766e-01 1.48913e-01 ; corrected from Cheatham (old 4.40104e-01 4.18400e-01)
Na 11 22.99 0.0000 A 2.43934e-01 3.65846e-01 ; corrected from Cheatham (old 3.32840e-01 1.15897e-02)
K 19 39.10 0.0000 A 3.03796e-01 8.10369e-01 ; corrected from Cheatham (old 4.73602e-01 1.37235e-03)
Rb 37 85.47 0.0000 A 3.23040e-01 1.37161e+00 ; corrected from Cheatham (old 5.26699e-01 7.11280e-04)
Cs 55 132.91 0.0000 A 3.52083e-01 1.70096e+00 ; corrected from Cheatham (old 6.04920e-01 3.37230e-04)
Li 3 6.94 0.0000 A 1.82630e-01 1.17108e-01 ; corrected from Cheatham (old 2.02590e-01 7.65672e-02)
MG 12 24.305 0.0000 A 2.77000e-01 1.23428e-02 ; MG parameters from Villa (old: 1.41225e-01 3.74342e+00)
[ 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
CB CT 1 0.15100 265265.6 ; shape reagent; based on CA CT; 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
CA N* 1 0.13740 364844.8 ; shape reagent; based on CB N*; 7,(1986),230; ADE,GUA
CB NB 1 0.13910 346435.2 ; 7,(1986),230; ADE,GUA
CA NB 1 0.13910 346435.2 ; shape reagent; based on CB NB; 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
CT O 1 0.14100 267776.0 ; shape reagent; based on CT OS, 7,(1986),230; NUCLEIC ACIDS
C CY 1 0.14580 334720.0 ; shape reagent; based on CT-CY (Howard et al JCC.16,243,1995)
CY NY 1 0.11500 502080.0 ; shape reagent; Howard et al JCC,16,243,1995
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
CA NO 1 0.14690 215375.6 ; shape reagent; gaff2, based on no-o, SOURCE1_SOURCE5 4403 0.0099
NO O2 1 0.12260 307900.6 ; shape reagent; gaff2, based on no-o, SOURCE1_SOURCE5 4403 0.0099
;
; 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 ;
CA C O 1 128.800 669.440 ; shape reagent; based on CB C O
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 ;
N* C OS 1 120.900 669.440 ; shape reagent; based on N* C O
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 ;
CB CB CT 1 120.000 585.760 ; shape reagent; based on CA CA CT
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 ;
CA CA NO 1 123.500 585.760 ; shape reagent; based on CB CA N2
CB CA NC 1 117.300 585.760 ;
CA CA NC 1 117.300 585.760 ; shape reagent; CB CA NC
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 CA 1 119.200 527.184 ; shape reagent; based on C CB CB; 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 ;
CA CA NB 1 132.400 585.760 ; shape reagent; based on CA CB NB
CB CB N* 1 106.200 585.760 ;
CB C N* 1 106.200 585.760 ; shape reagent; based on CB CB N*
CA CA N* 1 106.200 585.760 ; shape reagent; based on CB CB N*
CA CB N* 1 106.200 585.760 ; shape reagent; based on CB CB N*
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
H4 CA N* 1 123.050 418.400 ; shape reagent; based on H5 CK N*; new99
H5 CK NB 1 123.050 418.400 ; new99
HA CA NB 1 123.050 418.400 ; shape reagent; based on H5 CK NB; 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
HA CA NC 1 115.450 418.400 ; shape reagent; baed on H5 CQ NC; 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 ;
CT CT O 1 109.500 418.400 ; shape reagent; based on CT CT OS
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
H1 CT O 1 109.500 418.400 ; shape reagent; based on H1 CT OS; 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* CK 1 121.600 585.760 ; shape reagent; based on C N* CM
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 ;
CA N* CK 1 105.400 585.760 ; shape reagent; based on CB N* CK
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 ;
CA NB CK 1 103.800 585.760 ; shape reagent; based on CB NB CK
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
C CY NY 1 180.000 669.440 ; shape reagent; based on CT-CY-NY (Junmei et al, 1999)
CA C CY 1 110.000 527.184 ; shape reagent; based on CT-CT-CY (Junmei et al, 1999)
O C CY 1 110.000 418.400 ; shape reagent; based on OS-CT-CY (Junmei et al, 1999)
CT CB NC 1 121.500 585.760 ; shape reagent; based on CS-CA-NC
HC CT CB 1 109.500 418.400 ; shape reagent; based on HC-CT-CS (Junmei et al, 1999)
C N* CA 1 121.600 585.760 ; shape reagent; based on C -N*-CS
CA NO O2 1 117.760 719.146 ; shape reagent; gaff2, based on ca-no-o, SOURCE3_SOURCE5 886 0.2929
O2 NO O2 1 125.080 976.127 ; shape reagent; gaff2, based on o -no-o, SOURCE4_SOURCE5 1464 0.8585
C N* CB 1 121.600 585.760 ; shape reagent; based on C -N*-CS
C OS C 1 117.000 502.080 ; shape reagent; based on C -OS-CT (Junmei et al, 1999)
CB C OS 1 120.000 585.760 ; shape reagent; based on CA-C -OS, phosphotyrosine
;
; 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
CA CA CA HA 4 180.00 4.60240 2 ; shape reagent; General improper torsional angle (2 general atom types)
C CA CA CA 4 180.00 4.60240 2 ; shape reagent; Using AMBER default value
CA CY C O 4 180.00 43.93200 2 ; shape reagent; General improper torsional angle (2 general atom types)
CA CB CA HA 4 180.00 4.60240 2 ; shape reagent; General improper torsional angle (2 general atom types)
CA CB CB N* 4 180.00 4.60240 2 ; shape reagent; Using AMBER default value
C CB N* CT 4 180.00 4.60240 2 ; shape reagent; Using AMBER default value
N* O C OS 4 180.00 43.93200 2 ; shape reagent; General improper torsional angle (2 general atom types)
CB O C OS 4 180.00 43.93200 2 ; shape reagent; General improper torsional angle (2 general atom types)
C CA CB CB 4 180.00 4.60240 2 ; shape reagent; Using AMBER default value
CA CA CA NO 4 180.00 4.60240 2 ; shape reagent; Using AMBER default value
CA O2 NO O2 4 180.00 4.60240 2 ; shape reagent; Using AMBER default value
CA HA CA NC 4 180.00 4.60240 2 ; shape reagent; General improper torsional angle (2 general atom types)
CB CT CB NC 4 180.00 4.60240 2 ; shape reagent; Using AMBER default value
CB N* C O 4 180.00 43.93200 2 ; shape reagent; General improper torsional angle (2 general atom types)
C CA N* CK 4 180.00 4.60240 2 ; shape reagent; Using AMBER default value
CA H4 CA N* 4 180.00 4.60240 2 ; shape reagent; General improper torsional angle (2 general atom types)
CA HA CA NB 4 180.00 4.60240 2 ; shape reagent; General improper torsional angle (2 general atom types)
H5 N* CK NB 4 180.00 4.60240 2 ; shape reagent; General improper torsional angle (2 general atom types)
N* CB CB NC 4 180.00 4.60240 2 ; shape reagent; Using AMBER default value
NB C CB CB 4 180.00 4.60240 2 ; shape reagent; Using AMBER default value
NB CA CB CB 4 180.00 4.60240 2 ; shape reagent; Using AMBER default value
N* CB CA CB 4 180.00 4.60240 2 ; shape reagent; gromacs requires; Using AMBER default value
[ 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
;
;i j k l func
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 O 9 0.0 0.60250 3 ; shape reagent; based on OS CT CT OS; parm98, TC,PC,PAK
OS CT CT O 9 0.0 4.91620 2 ; shape reagent; based on OS CT CT OS; 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 O 9 0.0 1.04600 1 ; shape reagent; based on H1 CT CT OS; Junmei et al, 1999
H2 CT CT O 9 0.0 1.04600 1 ; shape reagent; based on H1 CT CT OS; 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 CB CT X 9 0.0 0.00000 0 ; shape reagent; based on X CA CT X; 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 CA N* X 9 180.0 6.90360 2 ; shape reagent; based on X CB N* X; JCC,7,(1986),230
X CB NB X 9 180.0 10.66920 2 ; JCC,7,(1986),230
X CA NB X 9 180.0 10.66920 2 ; shape reagent; based on X CB NB X; 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
X C CY X 9 0.0 0.00000 1 ; shape reagent; based on X -CT-CY-X (Junmei et al, 1999)
X CA NO X 9 180.0 2.51040 2 ; shape reagent; gaff2, based on X -ca-no-X
; 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:
; Modified RNA chi torsions in CHIOL
; 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:
[ implicit_genborn_params ]
; atype sar st pi gbr hct
;Br 0.1 1 1 0.125 0.85 ; H
C 0.172 1 1.554 0.1875 0.72 ; C
CA 0.18 1 1.037 0.1875 0.72 ; C
CB 0.172 0.012 1.554 0.1875 0.72 ; C
CC 0.172 1 1.554 0.1875 0.72 ; C
CN 0.172 0.012 1.554 0.1875 0.72 ; C
CR 0.18 1 1.073 0.1875 0.72 ; C
CT 0.18 1 1.276 0.190 0.72 ; C
CV 0.18 1 1.073 0.1875 0.72 ; C
CW 0.18 1 1.073 0.1875 0.72 ; C
C* 0.172 0.012 1.554 0.1875 0.72 ; C
H 0.1 1 1 0.115 0.85 ; H
HC 0.1 1 1 0.125 0.85 ; H
H1 0.1 1 1 0.125 0.85 ; H
HA 0.1 1 1 0.125 0.85 ; H
H4 0.1 1 1 0.115 0.85 ; H
H5 0.1 1 1 0.125 0.85 ; H
HO 0.1 1 1 0.105 0.85 ; H
HS 0.1 1 1 0.125 0.85 ; H
HP 0.1 1 1 0.125 0.85 ; H
N 0.155 1 1.028 0.17063 0.79 ; N
NA 0.155 1 1.028 0.17063 0.79 ; N
NB 0.155 1 1.215 0.17063 0.79 ; N
N2 0.16 1 1.215 0.17063 0.79 ; N
N3 0.16 1 1.215 0.1625 0.79 ; N
O 0.15 1 0.926 0.148 0.85 ; O
OH 0.152 1 1.080 0.1535 0.85 ; O
O2 0.17 1 0.922 0.148 0.85 ; O
S 0.18 1 1.121 0.1775 0.96 ; S
SH 0.18 1 1.121 0.1775 0.96 ; S
; masscenters for vsites do not have gbsa parameters
MNH3 0 0 0 0 0
MCH3 0 0 0 0 0
; Include chain topologies
;
; File 'SRP-motif_BzCN_GMX_RNA_chain_A.itp' was generated
; By user: vmlynsky (5837)
; On host: sirani.sbp.sissa.it
; At date: Thu Mar 23 14:16:07 2017
;
; This is a include topology file
;
; It was generated using program:
; pdb2gmx_mpi_d - VERSION 4.6.7
;
; Command line was:
; pdb2gmx_mpi_d -f SRP-motif_BzCN.pdb -o load.gro -p SRP-motif_BzCN_GMX.top -i posrestr.itp
;
; Force field was read from current directory or a relative path - path added.
;
[ moleculetype ]
; Name nrexcl
RNA_chain_A 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 C rtp RC5 q -0.3
1 OH 1 C O5' 1 -0.6223 16 ; qtot -0.6223
2 HO 1 C H5T 2 0.4295 1.008 ; qtot -0.1928
3 CI 1 C C5' 3 0.0558 12.01 ; qtot -0.137
4 H1 1 C H5'1 4 0.0679 1.008 ; qtot -0.0691
5 H1 1 C H5'2 5 0.0679 1.008 ; qtot -0.0012
6 CT 1 C C4' 6 0.1065 12.01 ; qtot 0.1053
7 H1 1 C H4' 7 0.1174 1.008 ; qtot 0.2227
8 OS 1 C O4' 8 -0.3548 16 ; qtot -0.1321
9 CT 1 C C1' 9 0.0066 12.01 ; qtot -0.1255
10 H2 1 C H1' 10 0.2029 1.008 ; qtot 0.0774
11 N* 1 C N1 11 -0.0484 14.01 ; qtot 0.029
12 CM 1 C C6 12 0.0053 12.01 ; qtot 0.0343
13 H4 1 C H6 13 0.1958 1.008 ; qtot 0.2301
14 CM 1 C C5 14 -0.5215 12.01 ; qtot -0.2914
15 HA 1 C H5 15 0.1928 1.008 ; qtot -0.0986
16 CA 1 C C4 16 0.8185 12.01 ; qtot 0.7199
17 N2 1 C N4 17 -0.953 14.01 ; qtot -0.2331
18 H 1 C H41 18 0.4234 1.008 ; qtot 0.1903
19 H 1 C H42 19 0.4234 1.008 ; qtot 0.6137
20 NC 1 C N3 20 -0.7584 14.01 ; qtot -0.1447
21 C 1 C C2 21 0.7538 12.01 ; qtot 0.6091
22 O 1 C O2 22 -0.6252 16 ; qtot -0.0161
23 CT 1 C C3' 23 0.2022 12.01 ; qtot 0.1861
24 H1 1 C H3' 24 0.0615 1.008 ; qtot 0.2476
25 CT 1 C C2' 25 0.067 12.01 ; qtot 0.3146
26 H1 1 C H2'1 26 0.0972 1.008 ; qtot 0.4118
27 OH 1 C O2' 27 -0.6139 16 ; qtot -0.2021
28 HO 1 C HO'2 28 0.4186 1.008 ; qtot 0.2165
29 OS 1 C O3' 29 -0.5246 16 ; qtot -0.3081
; residue 2 U rtp RU q -1.0
30 P 2 U P 30 1.1662 30.97 ; qtot 0.8581
31 O2 2 U O1P 31 -0.776 16 ; qtot 0.0821
32 O2 2 U O2P 32 -0.776 16 ; qtot -0.6939
33 OS 2 U O5' 33 -0.4989 16 ; qtot -1.193
34 CI 2 U C5' 34 0.0558 12.01 ; qtot -1.137
35 H1 2 U H5'1 35 0.0679 1.008 ; qtot -1.069
36 H1 2 U H5'2 36 0.0679 1.008 ; qtot -1.001
37 CT 2 U C4' 37 0.1065 12.01 ; qtot -0.8947
38 H1 2 U H4' 38 0.1174 1.008 ; qtot -0.7773
39 OS 2 U O4' 39 -0.3548 16 ; qtot -1.132
40 CT 2 U C1' 40 0.0674 12.01 ; qtot -1.065
41 H2 2 U H1' 41 0.1824 1.008 ; qtot -0.8823
42 N* 2 U N1 42 0.0418 14.01 ; qtot -0.8405
43 CM 2 U C6 43 -0.1126 12.01 ; qtot -0.9531
44 H4 2 U H6 44 0.2188 1.008 ; qtot -0.7343
45 CM 2 U C5 45 -0.3635 12.01 ; qtot -1.098
46 HA 2 U H5 46 0.1811 1.008 ; qtot -0.9167
47 C 2 U C4 47 0.5952 12.01 ; qtot -0.3215
48 O 2 U O4 48 -0.5761 16 ; qtot -0.8976
49 NA 2 U N3 49 -0.3549 14.01 ; qtot -1.252
50 H 2 U H3 50 0.3154 1.008 ; qtot -0.9371
51 C 2 U C2 51 0.4687 12.01 ; qtot -0.4684
52 O 2 U O2 52 -0.5477 16 ; qtot -1.016
53 CT 2 U C3' 53 0.2022 12.01 ; qtot -0.8139
54 H1 2 U H3' 54 0.0615 1.008 ; qtot -0.7524
55 CT 2 U C2' 55 0.067 12.01 ; qtot -0.6854
56 H1 2 U H2'1 56 0.0972 1.008 ; qtot -0.5882
57 OH 2 U O2' 57 -0.6139 16 ; qtot -1.202
58 HO 2 U HO'2 58 0.4186 1.008 ; qtot -0.7835
59 OS 2 U O3' 59 -0.5246 16 ; qtot -1.308
; residue 3 G rtp RG q -1.0
60 P 3 G P 60 1.1662 30.97 ; qtot -0.1419
61 O2 3 G O1P 61 -0.776 16 ; qtot -0.9179
62 O2 3 G O2P 62 -0.776 16 ; qtot -1.694
63 OS 3 G O5' 63 -0.4989 16 ; qtot -2.193
64 CI 3 G C5' 64 0.0558 12.01 ; qtot -2.137
65 H1 3 G H5'1 65 0.0679 1.008 ; qtot -2.069
66 H1 3 G H5'2 66 0.0679 1.008 ; qtot -2.001
67 CT 3 G C4' 67 0.1065 12.01 ; qtot -1.895
68 H1 3 G H4' 68 0.1174 1.008 ; qtot -1.777
69 OS 3 G O4' 69 -0.3548 16 ; qtot -2.132
70 CT 3 G C1' 70 0.0191 12.01 ; qtot -2.113
71 H2 3 G H1' 71 0.2006 1.008 ; qtot -1.912
72 N* 3 G N9 72 0.0492 14.01 ; qtot -1.863
73 CK 3 G C8 73 0.1374 12.01 ; qtot -1.726
74 H5 3 G H8 74 0.164 1.008 ; qtot -1.562
75 NB 3 G N7 75 -0.5709 14.01 ; qtot -2.133
76 CB 3 G C5 76 0.1744 12.01 ; qtot -1.958
77 C 3 G C6 77 0.477 12.01 ; qtot -1.481
78 O 3 G O6 78 -0.5597 16 ; qtot -2.041
79 NA 3 G N1 79 -0.4787 14.01 ; qtot -2.52
80 H 3 G H1 80 0.3424 1.008 ; qtot -2.177
81 CA 3 G C2 81 0.7657 12.01 ; qtot -1.412
82 N2 3 G N2 82 -0.9672 14.01 ; qtot -2.379
83 H 3 G H21 83 0.4364 1.008 ; qtot -1.942
84 H 3 G H22 84 0.4364 1.008 ; qtot -1.506
85 NC 3 G N3 85 -0.6323 14.01 ; qtot -2.138
86 CB 3 G C4 86 0.1222 12.01 ; qtot -2.016
87 CT 3 G C3' 87 0.2022 12.01 ; qtot -1.814
88 H1 3 G H3' 88 0.0615 1.008 ; qtot -1.752
89 CT 3 G C2' 89 0.067 12.01 ; qtot -1.685
90 H1 3 G H2'1 90 0.0972 1.008 ; qtot -1.588
91 OH 3 G O2' 91 -0.6139 16 ; qtot -2.202
92 HO 3 G HO'2 92 0.4186 1.008 ; qtot -1.783
93 OS 3 G O3' 93 -0.5246 16 ; qtot -2.308
; residue 4 U rtp RU q -1.0
94 P 4 U P 94 1.1662 30.97 ; qtot -1.142
95 O2 4 U O1P 95 -0.776 16 ; qtot -1.918
96 O2 4 U O2P 96 -0.776 16 ; qtot -2.694
97 OS 4 U O5' 97 -0.4989 16 ; qtot -3.193
98 CI 4 U C5' 98 0.0558 12.01 ; qtot -3.137
99 H1 4 U H5'1 99 0.0679 1.008 ; qtot -3.069
100 H1 4 U H5'2 100 0.0679 1.008 ; qtot -3.001
101 CT 4 U C4' 101 0.1065 12.01 ; qtot -2.895
102 H1 4 U H4' 102 0.1174 1.008 ; qtot -2.777
103 OS 4 U O4' 103 -0.3548 16 ; qtot -3.132
104 CT 4 U C1' 104 0.0674 12.01 ; qtot -3.065
105 H2 4 U H1' 105 0.1824 1.008 ; qtot -2.882
106 N* 4 U N1 106 0.0418 14.01 ; qtot -2.841
107 CM 4 U C6 107 -0.1126 12.01 ; qtot -2.953
108 H4 4 U H6 108 0.2188 1.008 ; qtot -2.734
109 CM 4 U C5 109 -0.3635 12.01 ; qtot -3.098
110 HA 4 U H5 110 0.1811 1.008 ; qtot -2.917
111 C 4 U C4 111 0.5952 12.01 ; qtot -2.322
112 O 4 U O4 112 -0.5761 16 ; qtot -2.898
113 NA 4 U N3 113 -0.3549 14.01 ; qtot -3.253
114 H 4 U H3 114 0.3154 1.008 ; qtot -2.937
115 C 4 U C2 115 0.4687 12.01 ; qtot -2.468
116 O 4 U O2 116 -0.5477 16 ; qtot -3.016
117 CT 4 U C3' 117 0.2022 12.01 ; qtot -2.814
118 H1 4 U H3' 118 0.0615 1.008 ; qtot -2.752
119 CT 4 U C2' 119 0.067 12.01 ; qtot -2.685
120 H1 4 U H2'1 120 0.0972 1.008 ; qtot -2.588
121 OH 4 U O2' 121 -0.6139 16 ; qtot -3.202
122 HO 4 U HO'2 122 0.4186 1.008 ; qtot -2.784
123 OS 4 U O3' 123 -0.5246 16 ; qtot -3.308
; residue 5 U rtp RU q -1.0
124 P 5 U P 124 1.1662 30.97 ; qtot -2.142
125 O2 5 U O1P 125 -0.776 16 ; qtot -2.918
126 O2 5 U O2P 126 -0.776 16 ; qtot -3.694
127 OS 5 U O5' 127 -0.4989 16 ; qtot -4.193
128 CI 5 U C5' 128 0.0558 12.01 ; qtot -4.137
129 H1 5 U H5'1 129 0.0679 1.008 ; qtot -4.069
130 H1 5 U H5'2 130 0.0679 1.008 ; qtot -4.001
131 CT 5 U C4' 131 0.1065 12.01 ; qtot -3.895
132 H1 5 U H4' 132 0.1174 1.008 ; qtot -3.777
133 OS 5 U O4' 133 -0.3548 16 ; qtot -4.132
134 CT 5 U C1' 134 0.0674 12.01 ; qtot -4.065
135 H2 5 U H1' 135 0.1824 1.008 ; qtot -3.882
136 N* 5 U N1 136 0.0418 14.01 ; qtot -3.841
137 CM 5 U C6 137 -0.1126 12.01 ; qtot -3.953
138 H4 5 U H6 138 0.2188 1.008 ; qtot -3.734
139 CM 5 U C5 139 -0.3635 12.01 ; qtot -4.098
140 HA 5 U H5 140 0.1811 1.008 ; qtot -3.917
141 C 5 U C4 141 0.5952 12.01 ; qtot -3.322