/usr/share/gromacs/top/encads.ff/ffbonded.itp is in gromacs-data 4.6.5-1build1.
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; i j func b0 kb
OW HW 1 0.10000 209200.0
OH HO 1 0.10000 209200.0
N1 HN 1 0.10000 209200.0
N2 HN 1 0.10000 209200.0
C1 H 1 0.10900 209200.0
C2 H 1 0.10900 209200.0
C3 H 1 0.10900 209200.0
CP H 1 0.10900 209200.0
C1 O 1 0.14370 209200.0
C2 O2 1 0.14370 209200.0
C2 OR 1 0.14370 209200.0
C1 OH 1 0.14390 209200.0
C2 OH 1 0.14390 209200.0
C3 OH 1 0.14390 209200.0
C1 N 1 0.14670 209200.0
C1 N1 1 0.14670 209200.0
C1 N2 1 0.14670 209200.0
C2 N 1 0.14670 209200.0
C2 N1 1 0.14670 209200.0
C2 N2 1 0.14670 209200.0
C3 N 1 0.14670 209200.0
C3 N1 1 0.14670 209200.0
C3 N2 1 0.14670 209200.0
CP N 1 0.14670 209200.0
CP N1 1 0.14670 209200.0
CP N2 1 0.14670 209200.0
C1 M1 1 0.14720 209200.0
C1 M2 1 0.14720 209200.0
C1 M3 1 0.14720 209200.0
C2 M1 1 0.14720 209200.0
C2 M2 1 0.14720 209200.0
C2 M3 1 0.14720 209200.0
C3 M1 1 0.14720 209200.0
C3 M2 1 0.14720 209200.0
C3 M3 1 0.14720 209200.0
C1 C1 1 0.15250 209200.0
C1 C2 1 0.15250 209200.0
C1 C3 1 0.15250 209200.0
C2 C2 1 0.15250 209200.0
C2 C3 1 0.15250 209200.0
C3 C3 1 0.15250 209200.0
CP CP 1 0.15190 209200.0
C1 CP 1 0.14980 209200.0
A6 H 1 0.10900 209200.0
A5 H 1 0.10900 209200.0
A7 H 1 0.10900 209200.0
A6 C1 1 0.15260 209200.0
A6 C2 1 0.15260 209200.0
A6 C3 1 0.15260 209200.0
A6 OH 1 0.13780 209200.0
A7 C1 1 0.15260 209200.0
A7 C2 1 0.15260 209200.0
A7 C3 1 0.15260 209200.0
Aprime C1 1 0.15260 209200.0
Abis C1 1 0.15260 209200.0
Aprime C2 1 0.15260 209200.0
Aprime C3 1 0.15260 209200.0
Abis C2 1 0.15260 209200.0
Abis C3 1 0.15260 209200.0
Aprime O 1 0.12360 418400.0
Aprime OH 1 0.12360 418400.0
Abis Obis 1 0.12230 418400.0
Aprime N 1 0.13220 418400.0
Aprime N1 1 0.13220 418400.0
Aprime N2 1 0.13220 418400.0
A5 N 1 0.13340 418400.0
A5 N1 1 0.13340 418400.0
A5 N2 1 0.13340 418400.0
A5 C1 1 0.15160 209200.0
A5 C2 1 0.15160 209200.0
A5 C3 1 0.15160 209200.0
A5 A5 1 0.13760 418400.0
A5 A7 1 0.14510 418400.0
A5 L5 1 0.13340 418400.0
A6 O 1 0.12280 418400.0
A6 O2 1 0.12280 418400.0
A6 OR 1 0.12280 418400.0
A6 A6 1 0.13890 418400.0
A6 A7 1 0.14110 418400.0
A6 M1 1 0.13350 418400.0
A6 M2 1 0.13350 418400.0
A6 M3 1 0.13350 418400.0
A7 N 1 0.13670 418400.0
A7 N2 1 0.13670 418400.0
A7 N1 1 0.13430 418400.0
A7 A7 1 0.13640 418400.0
SH H 1 0.13300 209200.0
S C2 1 0.18080 209200.0
S C3 1 0.18080 209200.0
SH C2 1 0.18080 209200.0
S S 1 0.20150 209200.0
M1 HN 1 0.10000 209200.0
M2 HN 1 0.10000 209200.0
M3 HN 1 0.10000 209200.0
A6 N 1 0.13550 418400.0
A6 N1 1 0.13550 418400.0
A6 N2 1 0.13550 418400.0
A6 L5 1 0.13550 418400.0
A6 L6 1 0.13550 418400.0
A7 L5 1 0.13670 418400.0
A7 L6 1 0.13670 418400.0
P OP 1 0.14800 418400.0
P O2 1 0.15940 209200.0
Y A6 1 0.13960 418400.0
Y Aprime 1 0.13960 418400.0
Y R 1 0.13840 418400.0
Y W 1 0.13840 418400.0
Z C2 1 0.15170 209200.0
Z C3 1 0.15170 209200.0
Z A6 1 0.14900 418400.0
Z Aprime 1 0.14900 418400.0
Z Y 1 0.14440 418400.0
Z Z 1 0.13570 418400.0
FE N 1 0.19800 58576.0
FE N1 1 0.19800 58576.0
FE N2 1 0.19800 58576.0
FE W 1 0.19800 58576.0
OF FE 1 0.16320 58576.0 ; iron-oxygen bond
OF OF 1 0.12240 418400.0
;[ constrainttypes ]
[ angletypes ]
; i j k func th0 cth
HW OW HW 1 109.47 502.08
C1 OH HO 1 110.00 502.08
C2 OH HO 1 110.00 502.08
C3 OH HO 1 110.00 502.08
Aprime OH HO 1 110.00 502.08
A6 OH HO 1 110.00 502.08
C1 C1 Abis 1 110.10 502.08
C2 C1 Abis 1 110.10 502.08
C3 C1 Abis 1 110.10 502.08
HN N2 HN 1 120.00 502.08
CP N1 HN 1 119.50 502.08
CP N2 HN 1 119.50 502.08
C1 N1 HN 1 119.50 502.08
C1 N2 HN 1 119.50 502.08
C2 N1 HN 1 119.50 502.08
C2 N2 HN 1 119.50 502.08
C3 N1 HN 1 119.50 502.08
C3 N2 HN 1 119.50 502.08
A6 N1 HN 1 119.60 502.08
A6 N2 HN 1 119.60 502.08
A5 N1 HN 1 119.60 502.08
A5 N2 HN 1 119.60 502.08
A7 N1 HN 1 119.60 502.08
A7 N2 HN 1 119.60 502.08
Aprime N1 HN 1 119.60 502.08
Aprime N2 HN 1 119.60 502.08
N2 Aprime N2 1 113.00 502.08
C2 Aprime C3 1 118.00 502.08
C1 N C1 1 112.40 502.08
C1 N C2 1 112.40 502.08
C1 N C3 1 112.40 502.08
C1 N1 CP 1 112.40 502.08
C1 N1 C1 1 112.40 502.08
C1 N1 C2 1 112.40 502.08
C1 N1 C3 1 112.40 502.08
C1 N2 CP 1 112.40 502.08
C1 N2 C1 1 112.40 502.08
C1 N2 C2 1 112.40 502.08
C1 N2 C3 1 112.40 502.08
C2 N C2 1 112.40 502.08
C2 N C3 1 112.40 502.08
C2 N1 C2 1 112.40 502.08
C2 N1 C3 1 112.40 502.08
C2 N2 C2 1 112.40 502.08
C2 N2 C3 1 112.40 502.08
C3 N C3 1 112.40 502.08
C3 N1 C3 1 112.40 502.08
C3 N2 C3 1 112.40 502.08
C1 N CP 1 112.40 502.08
A6 N C1 1 121.30 502.08
A6 N C2 1 121.30 502.08
A6 N C3 1 121.30 502.08
A6 N1 C1 1 121.30 502.08
A6 N1 C2 1 121.30 502.08
A6 N1 C3 1 121.30 502.08
A6 N2 C1 1 121.30 502.08
A6 N2 C2 1 121.30 502.08
A6 N2 C3 1 121.30 502.08
A5 N C1 1 121.30 502.08
A5 N C2 1 121.30 502.08
A5 N C3 1 121.30 502.08
A5 N1 C1 1 121.30 502.08
A5 N1 C2 1 121.30 502.08
A5 N1 C3 1 121.30 502.08
A5 N2 C1 1 121.30 502.08
A5 N2 C2 1 121.30 502.08
A5 N2 C3 1 121.30 502.08
A7 N C1 1 121.30 502.08
A7 N C2 1 121.30 502.08
A7 N C3 1 121.30 502.08
A7 N1 C1 1 121.30 502.08
A7 N1 C2 1 121.30 502.08
A7 N1 C3 1 121.30 502.08
A7 N2 C1 1 121.30 502.08
A7 N2 C2 1 121.30 502.08
A7 N2 C3 1 121.30 502.08
Aprime N C1 1 121.30 502.08
Aprime N C2 1 121.30 502.08
Aprime N C3 1 121.30 502.08
Aprime N1 C1 1 121.30 502.08
Aprime N1 C2 1 121.30 502.08
Aprime N1 C3 1 121.30 502.08
Aprime N2 C1 1 121.30 502.08
Aprime N2 C2 1 121.30 502.08
Aprime N2 C3 1 121.30 502.08
A5 N A5 1 108.00 1004.16
A5 N1 A5 1 108.00 1004.16
A5 N2 A5 1 108.00 1004.16
A5 N1 A7 1 108.00 1004.16
H C1 H 1 109.50 502.08
H C2 H 1 109.50 502.08
H C3 H 1 109.50 502.08
H CP H 1 109.50 502.08
O C1 H 1 109.00 502.08
OH C1 H 1 109.00 502.08
OH C2 H 1 109.00 502.08
OH C3 H 1 109.00 502.08
O2 C2 H 1 109.00 502.08
OR C2 H 1 109.00 502.08
O C1 C1 1 109.50 502.08
O C1 C2 1 109.50 502.08
O C1 C3 1 109.50 502.08
OH C1 C1 1 107.90 502.08
OH C1 C2 1 107.90 502.08
OH C1 C3 1 107.90 502.08
OH C2 C1 1 107.90 502.08
OH C2 C2 1 107.90 502.08
OH C2 C3 1 107.90 502.08
O2 C2 C1 1 109.50 502.08
O2 C2 C2 1 109.50 502.08
O2 C2 C3 1 109.50 502.08
OR C2 C1 1 109.50 502.08
OR C2 C2 1 109.50 502.08
OR C2 C3 1 109.50 502.08
C1 C1 H 1 109.50 502.08
C1 C2 H 1 109.50 502.08
C1 C3 H 1 109.50 502.08
C1 CP H 1 109.50 502.08
C2 C1 H 1 109.50 502.08
C2 C2 H 1 109.50 502.08
C2 C3 H 1 109.50 502.08
C3 C1 H 1 109.50 502.08
C3 C2 H 1 109.50 502.08
C3 C3 H 1 109.50 502.08
CP C1 H 1 109.50 502.08
CP CP H 1 109.50 502.08
N C1 H 1 109.50 502.08
N C2 H 1 109.50 502.08
N C3 H 1 109.50 502.08
N CP H 1 109.50 502.08
N1 CP H 1 109.50 502.08
N1 C1 H 1 109.50 502.08
N1 C2 H 1 109.50 502.08
N1 C3 H 1 109.50 502.08
N2 CP H 1 109.50 502.08
N2 C1 H 1 109.50 502.08
N2 C2 H 1 109.50 502.08
N2 C3 H 1 109.50 502.08
M1 C1 H 1 109.50 502.08
M1 C2 H 1 109.50 502.08
M1 C3 H 1 109.50 502.08
M2 C1 H 1 109.50 502.08
M2 C2 H 1 109.50 502.08
M2 C3 H 1 109.50 502.08
M3 C1 H 1 109.50 502.08
M3 C2 H 1 109.50 502.08
M3 C3 H 1 109.50 502.08
M1 C1 C1 1 111.00 502.08
M1 C1 C2 1 111.00 502.08
M1 C1 C3 1 111.00 502.08
M1 C2 C1 1 111.00 502.08
M1 C2 C2 1 111.00 502.08
M1 C2 C3 1 111.00 502.08
M2 C1 C1 1 111.00 502.08
M2 C1 C2 1 111.00 502.08
M2 C1 C3 1 111.00 502.08
M2 C2 C1 1 111.00 502.08
M2 C2 C2 1 111.00 502.08
M2 C2 C3 1 111.00 502.08
M3 C1 C1 1 111.00 502.08
M3 C1 C2 1 111.00 502.08
M3 C1 C3 1 111.00 502.08
M3 C2 C1 1 111.00 502.08
M3 C2 C2 1 111.00 502.08
M3 C2 C3 1 111.00 502.08
A6 C1 H 1 109.50 502.08
A6 C2 H 1 109.50 502.08
A6 C3 H 1 109.50 502.08
A5 C1 H 1 109.50 502.08
A5 C2 H 1 109.50 502.08
A5 C3 H 1 109.50 502.08
A7 C1 H 1 109.50 502.08
A7 C2 H 1 109.50 502.08
A7 C3 H 1 109.50 502.08
Aprime C1 H 1 109.50 502.08
Aprime C2 H 1 109.50 502.08
Aprime C3 H 1 109.50 502.08
Abis C2 H 1 109.50 502.08
Abis C3 H 1 109.50 502.08
Abis C1 H 1 109.50 502.08
C1 C1 N 1 109.10 502.08
C1 C1 N1 1 109.10 502.08
C1 C1 N2 1 109.10 502.08
C1 C2 N 1 109.10 502.08
C1 C2 N1 1 109.10 502.08
C1 C2 N2 1 109.10 502.08
C2 C1 N 1 109.10 502.08
C2 C1 N1 1 109.10 502.08
C2 C1 N2 1 109.10 502.08
C2 C2 N 1 109.10 502.08
C2 C2 N1 1 109.10 502.08
C2 C2 N2 1 109.10 502.08
C3 C1 N 1 109.10 502.08
C3 C1 N1 1 109.10 502.08
C3 C1 N2 1 109.10 502.08
C3 C2 N 1 109.10 502.08
C3 C2 N1 1 109.10 502.08
C3 C2 N2 1 109.10 502.08
CP C1 N 1 104.00 502.08
CP C1 N1 1 109.10 502.08
CP C1 N2 1 109.10 502.08
A6 C1 N 1 111.30 502.08
A6 C1 N1 1 111.30 502.08
A6 C1 N2 1 111.30 502.08
A6 C2 N 1 111.30 502.08
A6 C2 N1 1 111.30 502.08
A6 C2 N2 1 111.30 502.08
A5 C1 N 1 111.30 502.08
A5 C1 N1 1 111.30 502.08
A5 C1 N2 1 111.30 502.08
A5 C2 N 1 111.30 502.08
A5 C2 N1 1 111.30 502.08
A5 C2 N2 1 111.30 502.08
A7 C1 N 1 111.30 502.08
A7 C1 N1 1 111.30 502.08
A7 C1 N2 1 111.30 502.08
A7 C2 N 1 111.30 502.08
A7 C2 N1 1 111.30 502.08
A7 C2 N2 1 111.30 502.08
Aprime C1 N 1 111.30 502.08
Aprime C1 N1 1 111.30 502.08
Aprime C1 N2 1 111.30 502.08
Aprime C2 N 1 111.30 502.08
Aprime C2 N1 1 111.30 502.08
Aprime C2 N2 1 111.30 502.08
Abis C2 N 1 111.30 502.08
Abis C2 N1 1 111.30 502.08
Abis C2 N2 1 111.30 502.08
A6 C1 M1 1 111.30 502.08
A6 C1 M2 1 111.30 502.08
A6 C1 M3 1 111.30 502.08
A6 C2 M1 1 111.30 502.08
A6 C2 M2 1 111.30 502.08
A6 C2 M3 1 111.30 502.08
A5 C1 M1 1 111.30 502.08
A5 C1 M2 1 111.30 502.08
A5 C1 M3 1 111.30 502.08
A5 C2 M1 1 111.30 502.08
A5 C2 M2 1 111.30 502.08
A5 C2 M3 1 111.30 502.08
A7 C1 M1 1 111.30 502.08
A7 C1 M2 1 111.30 502.08
A7 C1 M3 1 111.30 502.08
A7 C2 M1 1 111.30 502.08
A7 C2 M2 1 111.30 502.08
A7 C2 M3 1 111.30 502.08
Aprime C1 M1 1 111.30 502.08
Aprime C1 M2 1 111.30 502.08
Aprime C1 M3 1 111.30 502.08
Aprime C2 M1 1 111.30 502.08
Aprime C2 M2 1 111.30 502.08
Aprime C2 M3 1 111.30 502.08
Abis C2 M1 1 111.30 502.08
Abis C2 M2 1 111.30 502.08
Abis C2 M3 1 111.30 502.08
Abis C1 M1 1 111.30 502.08
Abis C1 M2 1 111.30 502.08
Abis C1 M3 1 111.30 502.08
Abis C1 N 1 111.30 502.08
Abis C1 N1 1 111.30 502.08
Abis C1 N2 1 111.30 502.08
C1 C1 C1 1 111.40 502.08
C1 C1 C2 1 111.40 502.08
C1 C1 C3 1 111.40 502.08
C1 C2 C1 1 111.40 502.08
C1 C2 C2 1 111.40 502.08
C1 C2 C3 1 111.40 502.08
C1 CP CP 1 107.20 502.08
C2 C1 C2 1 111.40 502.08
C2 C1 C3 1 111.40 502.08
C2 C2 C2 1 111.40 502.08
C2 C2 C3 1 111.40 502.08
C3 C1 C3 1 111.40 502.08
C3 C2 C3 1 111.40 502.08
CP CP CP 1 103.90 502.08
N CP CP 1 105.10 502.08
N1 CP CP 1 105.10 502.08
N2 CP CP 1 105.10 502.08
Aprime N CP 1 125.80 502.08
A6 C1 C1 1 114.10 502.08
A6 C1 C2 1 114.10 502.08
A6 C1 C3 1 114.10 502.08
A6 C2 C1 1 114.10 502.08
A6 C2 C2 1 114.10 502.08
A6 C2 C3 1 114.10 502.08
A5 C1 C1 1 113.90 502.08
A5 C1 C2 1 113.90 502.08
A5 C1 C3 1 113.90 502.08
A5 C2 C1 1 113.90 502.08
A5 C2 C2 1 113.90 502.08
A5 C2 C3 1 113.90 502.08
A7 C1 C1 1 110.10 502.08
A7 C1 C2 1 110.10 502.08
A7 C1 C3 1 110.10 502.08
A7 C2 C1 1 110.10 502.08
A7 C2 C2 1 110.10 502.08
A7 C2 C3 1 110.10 502.08
Aprime C1 C1 1 110.10 502.08
Aprime C1 C2 1 110.10 502.08
Aprime C1 C3 1 110.10 502.08
Aprime C1 CP 1 111.90 502.08
Abis C1 CP 1 110.10 502.08
Aprime C2 C1 1 110.10 502.08
Aprime C2 C2 1 110.10 502.08
Aprime C2 C3 1 110.10 502.08
Abis C2 C1 1 110.10 502.08
Abis C2 C2 1 110.10 502.08
Abis C2 C3 1 110.10 502.08
S C2 C1 1 115.50 502.08
S C2 C2 1 115.50 502.08
S C2 C3 1 115.50 502.08
SH C2 C1 1 115.50 502.08
SH C2 C2 1 115.50 502.08
SH C2 C3 1 115.50 502.08
S C2 H 1 110.00 502.08
S C3 H 1 110.00 502.08
SH C2 H 1 110.00 502.08
C2 SH H 1 110.00 502.08
H A6 H 1 120.00 502.08
H A5 H 1 120.00 502.08
H A7 H 1 120.00 502.08
A6 A6 H 1 120.00 502.08
A6 A7 H 1 120.00 502.08
A5 A5 H 1 126.00 502.08
A5 A7 H 1 120.00 502.08
A7 A6 H 1 120.00 502.08
A7 A5 H 1 126.00 502.08
A7 A7 H 1 120.00 502.08
O A6 O 1 120.00 502.08
O Aprime O 1 120.00 502.08
OH Aprime O 1 120.00 502.08
O2 A6 O 1 120.00 502.08
OR A6 O 1 120.00 502.08
N A6 H 1 120.00 502.08
N A5 H 1 126.00 502.08
N A7 H 1 120.00 502.08
N1 A6 H 1 120.00 502.08
N1 A5 H 1 126.00 502.08
N1 A7 H 1 120.00 502.08
N2 A6 H 1 120.00 502.08
N2 A5 H 1 126.00 502.08
N2 A7 H 1 120.00 502.08
N Aprime O 1 123.50 1004.16
N1 Aprime O 1 123.50 1004.16
N2 Aprime O 1 123.50 1004.16
C1 Aprime O 1 121.00 502.08
C1 Aprime OH 1 121.00 502.08
C2 Aprime O 1 121.00 502.08
C2 Aprime OH 1 121.00 502.08
C3 Aprime O 1 121.00 502.08
C3 Aprime C3 1 121.00 502.08
C1 Aprime N 1 115.50 502.08
C1 Aprime N1 1 115.50 502.08
C1 Aprime N2 1 115.50 502.08
C2 Aprime N 1 115.50 502.08
C2 Aprime N1 1 115.50 502.08
C2 Aprime N2 1 115.50 502.08
C3 Aprime N 1 115.50 502.08
C3 Aprime N1 1 115.50 502.08
C3 Aprime N2 1 115.50 502.08
Obis Abis C1 1 117.70 502.08
Obis Abis C2 1 117.70 502.08
Obis Abis C3 1 117.70 502.08
Obis Abis Obis 1 124.60 1004.16
C2 A5 A5 1 126.00 502.08
C2 A5 L5 1 126.00 502.08
L5 A5 H 1 126.00 502.08
C2 A5 A7 1 126.00 502.08
A5 A5 N 1 108.00 1004.16
A5 A5 N1 1 108.00 1004.16
A5 A5 N2 1 108.00 1004.16
A5 A5 L5 1 108.00 1004.16
N1 A5 L5 1 108.00 1004.16
C2 A5 N1 1 126.00 502.08
A7 A5 A5 1 108.00 1004.16
M1 A6 M1 1 120.00 1004.16
M1 A6 M2 1 120.00 1004.16
M1 A6 M3 1 120.00 1004.16
M2 A6 M2 1 120.00 1004.16
M2 A6 M3 1 120.00 1004.16
M3 A6 M3 1 120.00 1004.16
A6 A6 C1 1 120.10 502.08
A6 A6 C2 1 120.10 502.08
A6 A6 C3 1 120.10 502.08
A6 A6 A6 1 120.00 1004.16
A6 A6 OH 1 118.40 502.08
A7 A6 A6 1 120.00 1004.16
A5 A7 A7 1 108.00 1004.16
A7 A7 A6 1 120.00 1004.16
A5 A7 A6 1 132.00 1004.16
N A7 A6 1 132.00 502.08
N1 A7 A6 1 132.00 502.08
N2 A7 A6 1 132.00 502.08
N1 A7 A7 1 108.00 1004.16
L5 A7 A6 1 132.00 502.08
L6 A7 A6 1 132.00 502.08
C2 S C2 1 99.10 502.08
C2 S C3 1 99.10 502.08
S S C2 1 104.30 502.08
HN M2 HN 1 120.00 502.08
HN M3 HN 1 109.50 502.08
C1 M1 HN 1 119.50 502.08
C1 M2 HN 1 119.50 502.08
C1 M3 HN 1 109.50 502.08
C2 M1 HN 1 119.50 502.08
C2 M2 HN 1 119.50 502.08
C2 M3 HN 1 109.50 502.08
C3 M1 HN 1 119.50 502.08
C3 M2 HN 1 119.50 502.08
C3 M3 HN 1 109.50 502.08
A6 M1 HN 1 119.60 502.08
A6 M2 HN 1 119.60 502.08
A6 M3 HN 1 119.60 502.08
A6 M1 C1 1 123.20 502.08
A6 M1 C2 1 123.20 502.08
A6 M1 C3 1 123.20 502.08
A6 M2 C1 1 123.20 502.08
A6 M2 C2 1 123.20 502.08
A6 M2 C3 1 123.20 502.08
A6 M3 C1 1 123.20 502.08
A6 M3 C2 1 123.20 502.08
A6 M3 C3 1 123.20 502.08
A5 L5 A5 1 108.00 1004.16
A6 N1 A6 1 120.00 502.08
OH C1 N 1 109.50 502.08
OH C1 N1 1 109.50 502.08
OH C1 N2 1 109.50 502.08
C3 A7 A6 1 108.86 502.08
C3 A7 A7 1 132.53 502.08
L5 A7 A7 1 108.00 502.08
A7 A7 L6 1 120.00 502.08
A5 L5 A7 1 108.00 502.08
A6 L5 A7 1 119.33 502.08
N1 A5 N1 1 108.00 1004.16
Y A6 H 1 120.00 502.08
Z C2 H 1 110.00 502.08
Z C3 H 1 110.00 502.08
Z A6 H 1 120.00 502.08
A6 N FE 1 120.00 502.08
A6 N1 FE 1 120.00 502.08
A6 N2 FE 1 120.00 502.08
A5 N FE 1 120.00 502.08
A5 N1 FE 1 120.00 502.08
A5 N2 FE 1 120.00 502.08
A7 N FE 1 120.00 502.08
A7 N1 FE 1 120.00 502.08
A7 N2 FE 1 120.00 502.08
Aprime N FE 1 120.00 502.08
Aprime N1 FE 1 120.00 502.08
Aprime N2 FE 1 120.00 502.08
Y R Y 1 105.40 1004.16
Y A6 Y 1 124.50 502.08
Y Aprime Y 1 124.50 502.08
Y W Y 1 105.40 502.08
FE W Y 1 127.30 502.08
R Y A6 1 125.50 1004.16
R Y Aprime 1 125.50 1004.16
W Y A6 1 125.20 1004.16
W Y Aprime 1 125.20 1004.16
Z Y A6 1 124.20 1004.16
Z Y Aprime 1 124.20 1004.16
Z Y R 1 109.50 1004.16
Z Y W 1 109.50 1004.16
Y Z C2 1 125.40 502.08
Y Z C3 1 125.40 502.08
Y Z A6 1 124.40 1004.16
Y Z Aprime 1 124.40 1004.16
Z Z C2 1 127.50 502.08
Z Z C3 1 127.50 502.08
Z Z A6 1 128.40 1004.16
Z Z Aprime 1 128.40 1004.16
Z Z Y 1 107.00 1004.16
Z C2 C1 1 109.50 502.08
Z C2 C2 1 109.50 502.08
Z C2 C3 1 109.50 502.08
Z A6 A6 1 120.00 1004.16
Z A6 A7 1 120.00 1004.16
W FE N 1 90.00 502.08
W FE N1 1 90.00 502.08
W FE N2 1 90.00 502.08
W FE W 1 180.00 502.08
OF FE N 1 180.00 502.08
OF FE N1 1 180.00 502.08
OF FE N2 1 180.00 502.08
OF FE W 1 90.00 502.08
OF OF FE 1 120.00 502.08
[ dihedraltypes ]
; Encad proper dihedrals. Note that there is a difference pf
; sign in the cosine definition between Gromacs and Encad. All angle values
; here are thus offset 180 degrees.
; i l func q0 cq
C1 A6 A6 H 1 180.00 167.36 1
C2 A6 A6 H 1 180.00 167.36 1
C2 A5 A5 H 1 180.00 167.36 1
C2 A5 A7 H 1 180.00 167.36 1
C3 A6 A6 H 1 180.00 167.36 1
C3 A7 A6 H 1 180.00 167.36 1
C3 A7 A7 H 1 180.00 167.36 1
C2 A5 A7 A6 1 180.00 167.36 1
H A6 N C1 1 180.00 167.36 1
A6 A6 A6 H 1 0.00 167.36 1
L5 A7 A7 L5 1 0.00 167.36 1
L5 A7 A7 L6 1 0.00 167.36 1
L6 A7 A7 L6 1 0.00 167.36 1
N A7 A6 A6 1 0.00 167.36 1
N1 A7 A6 A6 1 0.00 167.36 1
N2 A7 A6 A6 1 0.00 167.36 1
N1 A7 A7 A6 1 0.00 167.36 1
A6 A7 L5 A5 1 180.00 83.68 2
A7 A7 N1 A5 1 180.00 167.36 1
Aprime N C1 Aprime 1 0.00 0.00 0 ; will be removed by grompp
Aprime N C2 Aprime 1 0.00 0.00 0 ; will be removed by grompp
Aprime N1 C1 Aprime 1 0.00 0.00 0 ; will be removed by grompp
Aprime N1 C2 Aprime 1 0.00 0.00 0 ; will be removed by grompp
Aprime N2 C1 Aprime 1 0.00 0.00 0 ; will be removed by grompp
Aprime N2 C2 Aprime 1 0.00 0.00 0 ; will be removed by grompp
HN N2 Aprime N2 1 180.00 41.84 2 ; not present in aanahn
C1 Aprime N C1 1 180.00 41.84 2
C1 Aprime N C2 1 180.00 41.84 2
C1 Aprime N C3 1 180.00 41.84 2
C1 Aprime N1 C1 1 180.00 41.84 2
C1 Aprime N1 C2 1 180.00 41.84 2
C1 Aprime N1 C3 1 180.00 41.84 2
C1 Aprime N2 C1 1 180.00 41.84 2
C1 Aprime N2 C2 1 180.00 41.84 2
C1 Aprime N2 C3 1 180.00 41.84 2
C2 Aprime N C1 1 180.00 41.84 2
C2 Aprime N C2 1 180.00 41.84 2
C2 Aprime N C3 1 180.00 41.84 2
C2 Aprime N1 C1 1 180.00 41.84 2
C2 Aprime N1 C2 1 180.00 41.84 2
C2 Aprime N1 C3 1 180.00 41.84 2
C2 Aprime N2 C1 1 180.00 41.84 2
C2 Aprime N2 C2 1 180.00 41.84 2
C2 Aprime N2 C3 1 180.00 41.84 2
C3 Aprime N C1 1 180.00 41.84 2
C3 Aprime N C2 1 180.00 41.84 2
C3 Aprime N C3 1 180.00 41.84 2
C3 Aprime N1 C1 1 180.00 41.84 2
C3 Aprime N1 C2 1 180.00 41.84 2
C3 Aprime N1 C3 1 180.00 41.84 2
C3 Aprime N2 C1 1 180.00 41.84 2
C3 Aprime N2 C2 1 180.00 41.84 2
C3 Aprime N2 C3 1 180.00 41.84 2
C1 Aprime N1 HN 1 180.00 41.84 2
C1 Aprime N2 HN 1 180.00 41.84 2
C2 Aprime N1 HN 1 180.00 41.84 2
C2 Aprime N2 HN 1 180.00 41.84 2
C3 Aprime N1 HN 1 180.00 41.84 2
C3 Aprime N2 HN 1 180.00 41.84 2
C1 A6 A6 A6 1 0.00 334.72 1
C2 A6 A6 A6 1 0.00 334.72 1
C3 A6 A6 A6 1 0.00 334.72 1
A6 A6 A6 A6 1 180.00 334.72 1
N C1 CP CP 1 180.00 41.84 1
N1 C1 CP CP 1 180.00 41.84 1
N2 C1 CP CP 1 180.00 41.84 1
C1 Aprime N CP 1 180.00 41.84 2
C2 Aprime N CP 1 180.00 41.84 2
C3 Aprime N CP 1 180.00 41.84 2
Aprime N CP CP 1 0.00 41.84 1
C1 A6 A6 X 1 180.00 41.84 2
C2 A6 A6 X 1 180.00 41.84 2
C2 A5 A5 X 1 180.00 41.84 2
C2 A5 A7 X 1 180.00 41.84 2
C3 A6 A6 X 1 180.00 41.84 2
C3 A7 A6 X 1 180.00 41.84 2
C3 A7 A7 X 1 180.00 41.84 2
X A5 N C1 1 0.00 167.36 1
X A5 N C2 1 0.00 167.36 1
X A5 N C3 1 0.00 167.36 1
X A5 N1 C1 1 0.00 167.36 1
X A5 N1 C2 1 0.00 167.36 1
X A5 N1 C3 1 0.00 167.36 1
X A5 N2 C1 1 0.00 167.36 1
X A5 N2 C2 1 0.00 167.36 1
X A5 N2 C3 1 0.00 167.36 1
C2 A5 N1 X 1 0.00 167.36 1
X A6 N C1 1 0.00 167.36 1
X A6 N C2 1 0.00 167.36 1
X A6 N C3 1 0.00 167.36 1
X A7 N C1 1 180.00 167.36 1
X A7 N C2 1 180.00 167.36 1
X A7 N C3 1 180.00 167.36 1
X A7 N1 C1 1 180.00 167.36 1
X A7 N1 C2 1 180.00 167.36 1
X A7 N1 C3 1 180.00 167.36 1
X A7 N2 C1 1 180.00 167.36 1
X A7 N2 C2 1 180.00 167.36 1
X A7 N2 C3 1 180.00 167.36 1
S S C2 X 1 0.00 0.00 0 ; will be removed by grompp
X A6 A6 X 1 180.00 167.36 1
X A6 A7 X 1 180.00 167.36 1
X A5 A5 X 1 180.00 167.36 1
X A5 A7 X 1 180.00 167.36 1
X A7 A7 X 1 180.00 167.36 1
X A5 N X 1 180.00 334.72 2
X A5 N1 X 1 180.00 334.72 2
X A5 N2 X 1 180.00 334.72 2
X A5 L5 X 1 180.00 41.84 2
X A6 N X 1 180.00 167.36 1
X A6 N1 X 1 180.00 167.36 1
X A6 N2 X 1 180.00 167.36 1
X A6 L5 X 1 180.00 167.36 1
X A6 L6 X 1 180.00 167.36 1
X A7 L5 X 1 180.00 167.36 1
X A7 L6 X 1 180.00 167.36 1
X P O2 X 1 0.00 8.368 3
X P OP X 1 0.00 8.368 3
X N C1 X 1 0.00 0.00 0 ; will be removed by grompp
X N C2 X 1 0.00 0.00 0 ; will be removed by grompp
X N C3 X 1 0.00 0.00 0 ; will be removed by grompp
X N CP X 1 0.00 0.00 0 ; will be removed by grompp
X N1 C1 X 1 0.00 0.00 0 ; will be removed by grompp
X N1 C2 X 1 0.00 0.00 0 ; will be removed by grompp
X N1 C3 X 1 0.00 0.00 0 ; will be removed by grompp
X N1 CP X 1 0.00 0.00 0 ; will be removed by grompp
X N2 C1 X 1 0.00 0.00 0 ; will be removed by grompp
X N2 C2 X 1 0.00 0.00 0 ; will be removed by grompp
X N2 C3 X 1 0.00 0.00 0 ; will be removed by grompp
X N2 CP X 1 0.00 0.00 0 ; will be removed by grompp
X C1 O X 1 0.00 2.5104 3
X C1 OH X 1 0.00 2.5104 3
X C2 OH X 1 0.00 2.5104 3
X C2 O2 X 1 0.00 2.5104 3
X C2 OR X 1 0.00 2.5104 3
X C3 OH X 1 0.00 2.5104 3
X C1 C1 X 1 0.00 5.8576 3
X C1 C2 X 1 0.00 5.8576 3
X C1 C3 X 1 0.00 5.8576 3
X C2 C2 X 1 0.00 5.8576 3
X C2 C3 X 1 0.00 5.8576 3
X C3 C3 X 1 0.00 5.8576 3
X C1 CP X 1 180.00 5.8576 3
X CP CP X 1 180.00 5.8576 3
X C1 Aprime X 1 0.00 0.00 0 ; will be removed by grompp
X C2 Aprime X 1 0.00 0.00 0 ; will be removed by grompp
X C3 Aprime X 1 0.00 0.00 0 ; will be removed by grompp
X CP Aprime X 1 0.00 0.00 0 ; will be removed by grompp
X C1 A6 X 1 0.00 0.4184 6
X C1 A5 X 1 0.00 0.4184 6
X C1 A7 X 1 0.00 0.4184 6
X C1 Abis X 1 0.00 0.4184 6
X C2 A6 X 1 0.00 0.4184 6
X C2 A5 X 1 0.00 0.4184 6
X C2 A7 X 1 0.00 0.4184 6
X C2 Abis X 1 0.00 0.4184 6
X C3 A6 X 1 0.00 0.4184 6
X C3 A5 X 1 0.00 0.4184 6
X C3 A7 X 1 0.00 0.4184 6
X C3 Abis X 1 0.00 0.4184 6
X C1 M3 X 1 0.00 5.8576 3
X C2 M3 X 1 0.00 5.8576 3
X C3 M3 X 1 0.00 5.8576 3
X A6 O2 X 1 0.00 2.5104 3
X Aprime OH X 1 0.00 2.5104 3
X A6 OH X 1 0.00 2.5104 3
X A6 M1 X 1 180.00 41.84 2
X A6 M2 X 1 180.00 41.84 2
X A6 M3 X 1 180.00 41.84 2
X S C2 X 1 0.00 4.184 3
X S C3 X 1 0.00 4.184 3
X SH C2 X 1 0.00 4.184 3
X S S X 1 0.00 25.104 2
X M1 C1 X 1 0.00 5.8576 3
X M1 C2 X 1 0.00 5.8576 3
X M1 C3 X 1 0.00 5.8576 3
X M2 C1 X 1 0.00 5.8576 3
X M2 C2 X 1 0.00 5.8576 3
X M2 C3 X 1 0.00 5.8576 3
X Y A6 X 1 180.00 41.84 2
X Y Aprime X 1 180.00 41.84 2
X Y R X 1 180.00 83.68 2
X Y W X 1 180.00 83.68 2
X Z C2 X 1 0.00 0.4184 6
X Z C3 X 1 0.00 0.4184 6
X Z A6 X 1 180.00 41.84 2
X Z Aprime X 1 180.00 41.84 2
X Z Y X 1 180.00 83.68 2
X Z Z X 1 180.00 83.68 2
X FE N X 1 0.00 0.00 0 ; will be removed by grompp
X FE N1 X 1 0.00 0.00 0 ; will be removed by grompp
X FE N2 X 1 0.00 0.00 0 ; will be removed by grompp
X FE W X 1 0.00 0.00 0 ; will be removed by grompp
X OF FE X 1 0.00 0.00 0 ; will be removed by grompp
; Encad out-of-plane potentials are the same functional form as
; Gromacs proper dihedrals (i.e. cosine, but with shifted sign).
; Note that the atom order is different too; In Gromacs, the first atom
; of an improper is the center one, while it is the 3rd in Encad.
; Since they use the same type as proper dihedrals we use defines here
; to avoid mistakes in ambiguous cases.
;
; Note: the three parameters are repeated, to avoid having the free energy B state
; picked up from the default proper dihedral parameter types
; (grompp would give errors about non-matching multiplicity between A/B states)
;
; DNA
#define improper_X_X_P_X 180.0 8.368 3 180.0 8.368 3
#define improper_X_X_M2_X 180.0 8.368 2 180.0 8.368 2
; Proteins
#define improper_X_X_N_X 180.0 8.368 2 180.0 8.368 2
#define improper_X_X_C_X 180.0 8.368 3 180.0 8.368 3
#define improper_X_X_A_X 180.0 8.368 2 180.0 8.368 2
#define improper_A_X_C1_X 60.0 75.312 1 60.0 75.312 1
#define improper_A_X_C1_H -60.0 75.312 1 -60.0 75.312 1
#define improper_X_X_C1_A 60.0 75.312 1 60.0 75.312 1
#define improper_C3_C2_C1_C3 60.0 75.312 1 60.0 75.312 1
#define improper_C_C1_C1_C3 60.0 75.312 1 60.0 75.312 1
#define improper_C3_C1_C1_OH -60.0 75.312 1 -60.0 75.312 1
#define improper_C1_C2_C1_C3 -60.0 75.312 1 -60.0 75.312 1
#define improper_N_A_C1_C -60.0 75.312 1 -60.0 75.312 1
#define improper_M_A_C1_C -60.0 75.312 1 -60.0 75.312 1
#define improper_X_X_M_X 180.0 8.368 2 180.0 8.368 2
#define improper_X_X_M3_X 180.0 8.368 3 180.0 8.368 3
; Heme
#define improper_X_X_R_X 180.0 8.368 2 180.0 8.368 2
#define improper_X_X_W_X 180.0 8.368 2 180.0 8.368 2
#define improper_X_X_Y_X 180.0 8.368 2 180.0 8.368 2
#define improper_X_X_Z_X 180.0 8.368 2 180.0 8.368 2
#define improper_X_X_FE_X 180.0 0.000 4 180.0 0.000 4
#define improper_X_X_OF_X 180.0 8.368 2 180.0 8.368 2
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