/usr/share/gromacs/top/gmx2.ff/ffbonded.itp is in gromacs-data 4.5.5-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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; i j func b0 kb
C O 1 0.12300 502080.
C OM 1 0.12500 418400.
C OA 1 0.13600 376560.
C N 1 0.13300 418400.
C NT 1 0.13300 376560.
C NL 1 0.13300 376560.
C1 OA 1 0.14300 334720.
C1 N 1 0.14700 376560.
C1 NT 1 0.14700 376560.
C1 NL 1 0.14700 376560.
C1 C 1 0.15300 334720.
C1 C1 1 0.15300 334720.
C2 OM 1 0.14300 376560.
C2 OA 1 0.14300 334720.
C2 N 1 0.14700 376560.
C2 NT 1 0.14700 376560.
C2 NL 1 0.14700 376560.
C2 C 1 0.15300 334720.
C2 C1 1 0.15300 334720.
C2 C2 1 0.15300 334720.
C3 N 1 0.14700 376560.
C3 C 1 0.15300 334720.
C3 C1 1 0.15300 334720.
C3 C2 1 0.15300 334720.
CR51 NR5 1 0.13300 418400.
CR51 NR5* 1 0.13300 418400.
CR61 C2 1 0.13900 418400.
CR61 CR61 1 0.13900 418400.
CB O 1 0.12300 502080.
CB OA 1 0.13600 376560.
CB NT 1 0.13300 376560.
CB NR5 1 0.13300 418400.
CB NR5* 1 0.13300 418400.
CB NP 1 0.13800 418400.
CB C 1 0.15300 334720.
CB C2 1 0.15300 334720.
CB C3 1 0.15300 334720.
CB CR51 1 0.13300 418400.
CB CR61 1 0.13900 418400.
CB CB 1 0.13900 418400.
H N 1 0.10000 374468.
H NT 1 0.10000 374468.
H NL 1 0.10000 374468.
H NR5* 1 0.10000 374468.
HO OA 1 0.10000 313800.
HW OW 1 0.10000 418400.
S O 1 0.15000 376560.
S C2 1 0.18300 376560.
S C3 1 0.17800 376560.
S HS 1 0.13300 313800.
S S 1 0.20400 418400.
FE NR5 1 0.19800 418400.
FE NP 1 0.20900 418400.
NZ C 1 0.13400 376560.
NZ H 1 0.10000 374468.
NE C 1 0.13400 376560.
NE C2 1 0.14700 376560.
NE H 1 0.10000 374468.
P OM 1 0.14800 376560.
P OA 1 0.16100 251040.
OS C2 1 0.14300 251040.
OS P 1 0.16100 251040.
CS1 OA 1 0.14300 251040.
CS1 NR5* 1 0.14800 251040.
CS1 C2 1 0.15300 251040.
CS1 OS 1 0.14350 251040.
CS1 CS1 1 0.15200 251040.
NR6 CR61 1 0.13200 418400.
NR6 CB 1 0.13400 418400.
NR6* C2 1 0.14800 334720.
NR6* C3 1 0.14800 334720.
NR6* CR61 1 0.14000 334720.
NR6* CB 1 0.14000 334720.
NR6* H 1 0.10000 374468.
NR6* CS1 1 0.14800 334720.
CS2 OA 1 0.14300 251040.
CS2 CR61 1 0.13900 334720.
CS2 CB 1 0.13900 334720.
CS2 OS 1 0.14350 251040.
CS2 CS1 1 0.15200 251040.
CS2 NR6* 1 0.14000 334720.
SI C1 1 0.18700 251040.
SI OS 1 0.16300 251040.
F C 1 0.13600 418400.
CR5 HCR 1 0.10800 292880.
CR6 HCR 1 0.10800 292880.
CB CR6 1 0.13900 418400.
CR51 CR51 1 0.13300 418400.
NR6 C2 1 0.13400 418400.
; NR6* C2 1 0.13400 418400.
NR6* CR5 1 0.13400 418400.
CB CR5 1 0.13900 418400.
CR5 NR5 1 0.13300 418400.
CR5 NR5* 1 0.13300 418400.
CR6 C2 1 0.13900 418400.
CR6 CR6 1 0.13900 418400.
CP2 CP2 1 0.15300 334720.
CP3 CP2 1 0.15300 334720.
C CP2 1 0.15300 334720.
OS C 1 0.14350 251040.
C1 OS 1 0.14350 251040.
; Added by RMS & EAB, Oct 95
CR5 HC 1 0.10900 292880.
C1 HC 1 0.10900 292880.
C2 HC 1 0.10900 292880.
C3 HC 1 0.10900 292880.
; get the constraint distances
#include "ff_dum.itp"
[ constrainttypes ]
; now the constraints for the rigid NH3 groups
MNH3 C 2 DC_MNC1
MNH3 C1 2 DC_MNC2
MNH3 C2 2 DC_MNC2
MNH3 MNH3 2 DC_MNMN
; now the constraints for the rigid CH3 groups
MCH3 N 2 DC_MCN
MCH3 S 2 DC_MCS
MCH3 C 2 DC_MCC
MCH3 CB 2 DC_MCC
MCH3 C1 2 DC_MCC
MCH3 C2 2 DC_MCC
MCH3 NR6* 2 DC_MCNR
MCH3 MCH3 2 DC_MCMC
; and the angle-constraining bonds for OH and SH groups in proteins:
C2 HS 2 DC_CS
C2 HO 2 DC_CO
C1 HO 2 DC_CO
CB HO 2 DC_CO
C HO 2 DC_CO
P HO 2 DC_PO
[ angletypes ]
; i j k func tHC cth
HO OA C 1 109.500 397.480
HO OA C1 1 109.500 397.480
HO OA C2 1 109.500 397.480
HO OA CB 1 109.500 397.480
P OA HO 1 109.500 397.480
CS1 OA HO 1 109.500 397.480
CS2 OA HO 1 109.500 397.480
HW OW HW 1 109.500 502.080
C1 N C 1 122.000 502.080
C2 N C 1 122.000 502.080
C2 N C1 1 116.000 502.080
C3 N C 1 117.000 502.080
C3 N C1 1 125.000 502.080
C3 N C2 1 125.000 502.080
H N C 1 123.000 292.880
H N C1 1 115.000 376.560
H N C2 1 115.000 376.560
H N C3 1 120.000 376.560
H NT C 1 120.000 292.880
H NT C1 1 120.000 376.560
H NT C2 1 120.000 376.560
H NT CB 1 120.000 292.880
H NT H 1 120.000 334.720
H NL C 1 109.500 376.560
H NL C1 1 109.500 376.560
H NL C2 1 109.500 376.560
H NL H 1 109.500 334.720
CR51 NR5 CR51 1 108.000 418.400
CB NR5 CR51 1 108.000 418.400
FE NR5 CR51 1 125.000 251.040
CR51 NR5* CR51 1 108.000 418.400
CB NR5* CR51 1 108.000 418.400
CS1 NR5* CR51 1 126.000 418.400
CS1 NR5* CB 1 126.000 418.400
H NR5* CR51 1 126.000 376.560
H NR5* CB 1 126.000 376.560
CB NP CB 1 108.000 418.400
FE NP CB 1 126.000 418.400
OM C OM 1 126.000 502.080
OA C O 1 124.000 502.080
N C O 1 124.000 502.080
NT C O 1 124.000 502.080
NL C O 1 124.000 502.080
C1 C O 1 121.000 502.080
C1 C OM 1 117.000 502.080
C1 C OA 1 115.000 502.080
C1 C N 1 115.000 502.080
C1 C NT 1 115.000 502.080
C2 C O 1 121.000 502.080
C2 C OM 1 117.000 502.080
C2 C OA 1 115.000 502.080
C2 C N 1 115.000 502.080
C2 C NT 1 115.000 502.080
C2 C NL 1 115.000 502.080
C3 C O 1 121.000 502.080
C3 C N 1 115.000 502.080
CB C O 1 121.000 502.080
CB C N 1 115.000 502.080
CB C NT 1 115.000 502.080
NZ C NZ 1 120.000 502.080
NE C NZ 1 120.000 502.080
C C1 N 1 109.500 460.240
C C1 NT 1 109.500 460.240
C C1 NL 1 109.500 460.240
C1 C1 OA 1 109.500 460.240
C1 C1 N 1 109.500 460.240
C1 C1 NT 1 109.500 460.240
C1 C1 NL 1 109.500 460.240
C1 C1 C 1 109.500 460.240
C1 C1 C1 1 111.000 460.240
C2 C1 OA 1 109.500 460.240
C2 C1 N 1 109.500 460.240
C2 C1 NT 1 109.500 460.240
C2 C1 NL 1 109.500 460.240
C2 C1 C 1 109.500 460.240
C2 C1 C1 1 111.000 460.240
C2 C1 C2 1 109.500 460.240
C3 C1 OA 1 111.000 460.240
C3 C1 N 1 109.500 460.240
C3 C1 NT 1 109.500 460.240
C3 C1 NL 1 109.500 460.240
C3 C1 C 1 109.500 460.240
C3 C1 C1 1 111.000 460.240
C3 C1 C2 1 111.000 460.240
C3 C1 C3 1 111.000 460.240
SI C1 C3 1 109.500 460.240
C C2 N 1 109.500 460.240
C C2 NT 1 109.500 460.240
C C2 NL 1 109.500 460.240
C1 C2 OA 1 109.500 460.240
C1 C2 N 1 109.500 460.240
C1 C2 C 1 111.000 460.240
C1 C2 C1 1 109.500 460.240
C2 C2 OM 1 109.500 460.240
C2 C2 OA 1 109.500 460.240
C2 C2 N 1 109.500 460.240
C2 C2 NT 1 109.500 460.240
C2 C2 NL 1 109.500 460.240
C2 C2 C 1 111.000 460.240
C2 C2 C1 1 111.000 460.240
C2 C2 C2 1 111.000 460.240
C3 C2 OM 1 109.500 460.240
C3 C2 OA 1 111.000 460.240
C3 C2 C2 1 111.000 460.240
C3 C2 C1 1 111.000 460.240
CB C2 OM 1 109.500 460.240
CB C2 C1 1 111.000 460.240
CB C2 C2 1 111.000 460.240
S C2 C1 1 113.000 460.240
S C2 C2 1 113.000 460.240
NE C2 C2 1 109.500 460.240
OS C2 C1 1 111.000 460.240
NR6* C2 C1 1 111.000 460.240
NR6* C2 CB 1 109.500 460.240
NR6* C2 CS1 1 109.500 460.240
NR5* CR51 NR5 1 108.000 418.400
NR5* CR51 NR5* 1 108.000 418.400
CB CR51 NR5 1 108.000 418.400
CB CR51 NR5* 1 108.000 418.400
CR61 CR61 CR61 1 120.000 418.400
CB CR61 C2 1 126.000 418.400
CB CR61 CR61 1 120.000 418.400
CB CR61 CB 1 120.000 418.400
NR6 CR61 CB 1 120.000 418.400
NR6 CR61 NR6 1 120.000 418.400
NR6* CR61 CR61 1 120.000 418.400
NR6* CR61 CB 1 120.000 418.400
CS2 CR61 CR61 1 120.000 418.400
C2 CB NR5 1 126.000 418.400
C2 CB NR5* 1 126.000 418.400
CR51 CB NR5 1 108.000 418.400
CR51 CB NR5* 1 108.000 418.400
CR51 CB C2 1 126.000 418.400
CR61 CB OA 1 120.000 418.400
CR61 CB NT 1 120.000 418.400
CR61 CB NR5* 1 132.000 418.400
CR61 CB NP 1 126.000 418.400
CR61 CB C 1 120.000 418.400
CR61 CB C2 1 120.000 418.400
CR61 CB C3 1 120.000 418.400
CR61 CB CR61 1 120.000 418.400
CB CB O 1 120.000 418.400
CB CB NT 1 120.000 418.400
CB CB NR5 1 108.000 418.400
CB CB NR5* 1 108.000 418.400
CB CB NP 1 108.000 418.400
CB CB C2 1 126.000 418.400
CB CB C3 1 120.000 418.400
CB CB CR51 1 108.000 418.400
CB CB CR61 1 120.000 418.400
CB CB CB 1 120.000 418.400
NR6 CB O 1 120.000 418.400
NR6 CB NT 1 120.000 418.400
NR6 CB NR5* 1 132.000 418.400
NR6 CB C2 1 120.000 418.400
NR6 CB CR61 1 120.000 418.400
NR6 CB CB 1 120.000 418.400
NR6 CB NR6 1 120.000 418.400
NR6* CB O 1 120.000 418.400
NR6* CB NT 1 120.000 418.400
NR6* CB CR61 1 120.000 418.400
NR6* CB CB 1 120.000 418.400
NR6* CB NR6 1 120.000 418.400
NR6* CB NR6* 1 120.000 418.400
CS2 CB C 1 120.000 418.400
CS2 CB C2 1 120.000 418.400
CS2 CB CR61 1 120.000 418.400
CS2 CB NR6 1 120.000 418.400
C3 S O 1 107.000 460.240
C3 S C2 1 100.000 460.240
C3 S C3 1 97.000 460.240
HS S C2 1 96.000 397.480
S S C2 1 104.000 460.240
NP FE NR5 1 115.000 41.840
NP FE NP 1 90.000 418.400
H NZ C 1 120.000 292.880
H NZ H 1 120.000 334.720
C2 NE C 1 124.000 502.080
H NE C 1 120.000 292.880
H NE C2 1 116.000 376.560
OM P OM 1 120.000 585.760
OA P OM 1 109.600 397.480
OS P OM 1 109.600 397.480
OS P OA 1 103.000 397.480
OS P OS 1 103.000 397.480
P OS C2 1 120.000 397.480
P OS P 1 120.000 397.480
CS1 OS P 1 120.000 397.480
CS1 OS CS1 1 109.500 334.720
CS2 OS P 1 120.000 397.480
SI OS CS1 1 120.000 397.480
SI OS CS2 1 120.000 397.480
SI OS SI 1 155.000 397.480
OS CS1 NR5* 1 109.500 284.512
CS1 CS1 OA 1 109.500 284.512
CS1 CS1 NR5* 1 109.500 284.512
CS1 CS1 OS 1 109.500 284.512
CS1 CS1 CS1 1 109.500 251.040
NR6* CS1 C2 1 109.500 251.040
NR6* CS1 OS 1 109.500 284.512
NR6* CS1 CS1 1 109.500 251.040
CS2 CS1 OA 1 109.500 284.512
CS2 CS1 NR5* 1 109.500 284.512
CS2 CS1 C2 1 109.500 251.040
CS2 CS1 OS 1 109.500 284.512
CS2 CS1 CS1 1 109.500 251.040
CS2 CS1 NR6* 1 109.500 251.040
CB NR6 CR61 1 120.000 418.400
CB NR6 CB 1 120.000 418.400
C3 NR6* C2 1 120.000 418.400
CR61 NR6* CR61 1 120.000 418.400
CB NR6* C2 1 120.000 418.400
CB NR6* C3 1 120.000 418.400
CB NR6* CR61 1 120.000 418.400
CB NR6* CB 1 120.000 418.400
H NR6* C2 1 120.000 376.560
H NR6* CB 1 120.000 376.560
CS1 NR6* CR61 1 120.000 418.400
CS1 NR6* CB 1 120.000 418.400
CS1 NR6* H 1 120.000 376.560
CS2 NR6* CB 1 120.000 418.400
CS2 NR6* H 1 120.000 376.560
CB CS2 CR61 1 120.000 418.400
CS1 CS2 OA 1 109.500 284.512
CS1 CS2 OS 1 109.500 284.512
CS1 CS2 CS1 1 109.500 251.040
NR6* CS2 CB 1 120.000 418.400
NR6* CS2 CS1 1 120.000 418.400
C1 SI C1 1 109.500 397.480
OS SI C1 1 109.500 397.480
OS SI OS 1 109.500 397.480
F C F 1 107.600 460.240
C2 C F 1 111.400 460.240
C C2 OA 1 110.900 460.240
CS1 OS C2 1 112.900 397.480
OS C2 C2 1 107.900 460.240
CR6 CR6 HCR 1 120.000 376.560
CR5 CR6 HCR 1 120.000 376.560
CB CR6 HCR 1 120.000 376.560
CB CR5 HCR 1 120.000 376.560
NR5* CR5 HCR 1 120.000 376.560
NR5* CR6 HCR 1 120.000 376.560
CB CR51 CR51 1 108.000 418.400
H N H 1 109.500 334.720
C C1 OA 1 109.500 460.240
NL C1 C3 1 109.500 460.240
C2 S S 1 104.000 460.240
NR5* CB CR61 1 132.000 418.400
C1 CB NR5 1 126.000 418.400
; CB NR5 CR51 1 125.000 251.040
CB C NR6* 1 120.000 418.400
O C NR6* 1 120.000 418.400
C NR6* H 1 120.000 376.560
CB CB C 1 120.000 418.400
NR6 CB C 1 120.000 418.400
C NR6* C 1 120.000 418.400
NR6 CB NR6* 1 120.000 418.400
NR6 CB O 1 120.000 418.400
C2 NT C1 1 116.000 502.080
CR5 CB C2 1 126.000 418.400
CB CB CR5 1 108.000 418.400
CB CR5 NR5* 1 108.000 418.400
CB CB CR6 1 120.000 418.400
H NR5* CR5 1 126.000 376.560
CB NR5* CR5 1 108.000 418.400
CR6 CB NR5* 1 132.000 418.400
CB CR6 C2 1 126.000 418.400
CB CR6 CR6 1 120.000 418.400
CB CR6 CB 1 120.000 418.400
NR6 CR6 CB 1 120.000 418.400
CR6 CR6 CR6 1 120.000 418.400
CR6 CB C2 1 120.000 418.400
CR6 CB CR6 1 120.000 418.400
CB CR6 C2 1 126.000 418.400
CB CR6 CR6 1 120.000 418.400
CB CR6 CB 1 120.000 418.400
NR6 CR6 CB 1 120.000 418.400
NR6 CR6 NR6 1 120.000 418.400
NR6* CR6 CR6 1 120.000 418.400
NR6* CR6 CB 1 120.000 418.400
CS2 CR6 CR6 1 120.000 418.400
CR6 CB OA 1 120.000 418.400
CR6 CB NT 1 120.000 418.400
CR6 CB NR5* 1 132.000 418.400
CR6 CB NP 1 126.000 418.400
CR6 CB C 1 120.000 418.400
CR6 CB C2 1 120.000 418.400
CR6 CB C3 1 120.000 418.400
CR6 CB CR6 1 120.000 418.400
CP2 CP2 CP2 1 111.000 460.240
CP2 CP2 CP3 1 111.000 460.240
C CP2 CP2 1 111.000 460.240
O C CP2 1 121.000 502.080
OA C CP2 1 115.000 502.080
OS C CP2 1 121.000 502.080
; C1 C2 OS 1 121.000 502.080
C1 OS C 1 119.000 397.480
C2 C1 OS 1 106.000 397.480
OS C O 1 124.000 397.480
C2 OS C 1 119.000 397.480
; Added by DvdS, Oct 95
NL C1 HC 1 109.500 292.880 ; N-terminus
NT C1 HC 1 109.500 292.880 ; N-terminus
NR5* CB CR5 1 108.000 418.400 ; HIS stuff
CB CR5 HC 1 126.000 292.880
NR5* CR5 HC 1 126.000 292.880
NR5* CR5 NR5* 1 108.000 418.400
CR5 NR5* CR5 1 108.000 418.400
NR5 CB CR5 1 108.000 418.400
CB NR5 CR5 1 108.000 418.400
NR5 CR5 HC 1 126.000 292.880
NR5 CR5 NR5* 1 126.000 292.880
CB CR5 NR5 1 108.000 418.400
HC CR5 NR5 1 126.000 292.880
CR5 NR5 CR5 1 108.000 418.400
; Added by RMS & EAB, Oct 95
C1 C3 HC 1 109.500 292.880
C2 C3 HC 1 109.500 292.880
C3 C3 HC 1 109.500 292.880
S C3 HC 1 109.500 292.880
HC C3 HC 1 109.500 292.880
HC C2 HC 1 109.500 292.880
HC C1 HC 1 109.500 292.880
N C2 HC 1 109.500 292.880
NT C2 HC 1 109.500 292.880
NL C2 HC 1 109.500 292.880
C C2 HC 1 109.500 292.880
CB C2 HC 1 109.500 292.880
C1 C2 HC 1 109.500 292.880
C2 C2 HC 1 109.500 292.880
C3 C2 HC 1 109.500 292.880
S C2 HC 1 109.500 292.880
C C2 HC 1 109.500 292.880
NE C2 HC 1 109.500 292.880
OA C2 HC 1 109.500 292.880
C C1 HC 1 109.500 292.880
N C1 HC 1 109.500 292.880
OA C1 HC 1 109.500 292.880
C1 C1 HC 1 109.500 292.880
C2 C1 HC 1 109.500 292.880
C3 C1 HC 1 109.500 292.880
C C1 HC 1 109.500 292.880
[ dihedraltypes ]
; i l func q0 cq
NR5* NR5 2 0.000 167.360
NR5* NR5* 2 0.000 167.360
C O 2 0.000 167.360
C OM 2 0.000 167.360
C NT 2 0.000 167.360
C1 OA 2 35.264 334.720
C1 C1 2 35.264 334.720
C2 N 2 0.000 167.360
C2 NT 2 0.000 167.360
C2 C 2 0.000 167.360
C2 C1 2 35.264 334.720
C3 C1 2 35.264 334.720
CR51 NR5 2 0.000 167.360
CR51 NR5* 2 0.000 167.360
CR51 CR51 2 0.000 167.360
CR61 CR61 2 0.000 167.360
CB O 2 0.000 167.360
CB OA 2 0.000 167.360
CB NT 2 0.000 167.360
CB NR5 2 0.000 167.360
CB NR5* 2 0.000 167.360
CB NP 2 0.000 167.360
CB C 2 0.000 167.360
CB C2 2 0.000 167.360
CB C3 2 0.000 167.360
CB CR51 2 0.000 167.360
CB CR61 2 0.000 167.360
CB CB 2 0.000 167.360
H N 2 0.000 167.360
H NT 2 0.000 167.360
H NL 2 35.264 334.720
H NR5* 2 0.000 167.360
FE NP 2 0.000 167.360
NZ C 2 0.000 167.360
NE C 2 0.000 167.360
NE H 2 0.000 167.360
CS1 NR5* 2 0.000 167.360
CS1 C2 2 35.264 334.720
CS1 CB 2 0.000 167.360
CS1 CS1 2 35.264 334.720
NR6 CR61 2 0.000 167.360
NR6 CB 2 0.000 167.360
NR6 NR6 2 0.000 167.360
NR6* C2 2 0.000 167.360
NR6* C3 2 0.000 167.360
NR6* CR61 2 0.000 167.360
NR6* CB 2 0.000 167.360
NR6* H 2 0.000 167.360
NR6* CS1 2 0.000 167.360
NR6* NR6 2 0.000 167.360
NR6* NR6* 2 0.000 167.360
CS2 CB 2 0.000 167.360
CS2 CS1 2 35.264 334.720
CS2 NR6* 2 0.000 167.360
SI C1 2 35.264 334.720
C C1 2 0.000 167.360
NR6 C 2 0.000 167.360
C C 2 0.000 167.360
C NR6* 2 0.000 167.360
NR6 C2 2 0.000 167.360
CR5 HCR 2 0.000 167.360
CR6 HCR 2 0.000 167.360
CR5 CR5 2 0.000 167.360
CB CR5 2 0.000 167.360
NR6 CR5 2 0.000 167.360
NR6* CR5 2 0.000 167.360
CR5 NR5 2 0.000 167.360
CR5 NR5* 2 0.000 167.360
CR5 CR5 2 0.000 167.360
CB CR5 2 0.000 167.360
CB CR6 2 0.000 167.360
CR6 CR6 2 0.000 167.360
OS C 2 0.000 167.360
C O 2 0.000 167.360
C1 OS 2 35.264 334.720
C1 OA 2 35.264 334.720
; Added DvdS, Oct 95
CR5 HC 2 0.000 167.360
[ dihedraltypes ]
; j k func phi0 cp mult
C OA 1 180.000 16.736 2
C N 1 180.000 33.472 2
C NT 1 180.000 33.472 2
C NL 1 0.000 3.766 3
C1 OA 1 0.000 1.255 3
C1 N 1 180.000 0.418 6
C1 NT 1 0.000 3.766 6
C1 NL 1 0.000 3.766 3
C1 C 1 0.000 0.418 6
C1 C1 1 0.000 5.858 3
C2 OA 1 0.000 1.255 3
C2 N 1 180.000 0.418 6
C2 NT 1 0.000 3.766 6
C2 NL 1 0.000 3.766 3
C2 C 1 0.000 0.418 6
C2 C1 1 0.000 5.858 3
C2 C2 1 0.000 5.858 3
CB OA 1 180.000 7.113 2
CB NT 1 180.000 33.472 2
CB C 1 180.000 5.858 2
CB C2 1 0.000 0.418 6
CB CR61 1 180.000 41.840 2
S C2 1 0.000 2.929 3
S S 1 0.000 16.736 2
FE NR5 1 0.000 0.000 4
NZ C 1 180.000 33.472 2
NE C 1 180.000 33.472 2
NE C2 1 180.000 0.418 6
; two or three dihedral potentials are needed over some bonds,
; put the parameters in your topology manually
; P OA 1 0.000 1.046 3
; P OA 1 0.000 3.138 2
OS C2 1 0.000 3.766 3
; OS P 1 0.000 1.046 3
; OS P 1 0.000 3.138 2
CS1 OA 1 0.000 1.255 3
CS1 NR5* 1 0.000 0.000 2
CS1 C2 1 0.000 5.858 3
CS1 OS 1 0.000 3.766 3
; CS1 CS1 1 0.000 5.858 3
; CS1 CS1 1 0.000 0.418 2
; CS1 CS1 1 0.000 2.092 2
NR6 CB 1 180.000 33.472 2
NR6* C2 1 0.000 0.418 6
NR6* CB 1 180.000 33.472 2
NR6* CS1 1 0.000 0.000 2
CS2 OA 1 0.000 1.255 3
CS2 OS 1 0.000 3.766 3
; CS2 CS1 1 0.000 5.858 3
; CS2 CS1 1 0.000 0.418 2
; CS2 CS1 1 0.000 2.092 2
SI C1 1 0.000 5.858 3
SI OS 1 0.000 3.766 3
C CP2 1 0.000 0.418 6
C1 OS 1 0.000 3.766 3
C OS 1 0.000 3.766 3
CP2 CP2 1 0.000 0.418 6
; Added DvdS
C1 C3 1 180.000 0.418 6
C2 C3 1 180.000 0.418 6
S C3 1 180.000 0.418 6
[ dihedraltypes ]
CP2 CP2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495
C2 C2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495
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