/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp is in gromacs-data 5.0.2-1.
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; GROMOS bond-stretching parameters
;
;
; Bond type code
; Force constant
; Ideal bond length
; Examples of usage in terms of non-bonded atom types
;
;
; ICB(H)[N] CB[N] B0[N]
;
#define gb_1 0.1000 1.5700e+07
; H - OA 750
;
#define gb_2 0.1000 1.8700e+07
; H - N (all) 895
;
#define gb_3 0.1090 1.2300e+07
; HC - C 700
;
#define gb_4 0.112 3.7000e+07
; C - O (CO in heme) 2220
;
#define gb_5 0.1230 1.6600e+07
; C - O 1200
;
#define gb_6 0.1250 1.3400e+07
; C - OM 1000
;
#define gb_7 0.1320 1.2000e+07
; CR1 - NR (6-ring) 1000
;
#define gb_8 0.1330 8.8700e+06
; H - S 750
;
#define gb_9 0.1330 1.0600e+07
; C - NT, NL 900
;
#define gb_10 0.1330 1.1800e+07
; C, CR1 - N, NR, CR1, C (peptide, 5-ring) 1000
;
#define gb_11 0.1340 1.0500e+07
; C - N, NZ, NE 900
;
#define gb_12 0.1340 1.1700e+07
; C - NR (no H) (6-ring) 1000
;
#define gb_13 0.1360 1.0200e+07
; C - OA 900
;
#define gb_14 0.1380 1.1000e+07
; C - NR (heme) 1000
;
#define gb_15 0.1390 8.6600e+06
; CH2 - C, CR1 (6-ring) 800
;
#define gb_16 0.1390 1.0800e+07
; C, CR1 - CH2, C, CR1 (6-ring) 1000
;
#define gb_17 0.1400 8.5400e+06
; C, CR1, CH2 - NR (6-ring) 800
;
#define gb_18 0.1430 8.1800e+06
; CHn - OA 800
;
#define gb_19 0.1430 9.2100e+06
; CHn - OM 900
;
#define gb_20 0.1435 6.1000e+06
; CHn - OA (sugar) 600
;
#define gb_21 0.1470 8.7100e+06
; CHn - N, NT, NL, NZ, NE 900
;
#define gb_22 0.1480 5.7300e+06
; CHn - NR (5-ring) 600
;
#define gb_23 0.1480 7.6400e+06
; CHn - NR (6-ring) 800
;
#define gb_24 0.1480 8.6000e+06
; O, OM - P 900
;
#define gb_25 0.1500 8.3700e+06
; O - S 900
;
#define gb_26 0.1520 5.4300e+06
; CHn - CHn (sugar) 600
;
#define gb_27 0.1530 7.1500e+06
; C, CHn - C, CHn 800
;
#define gb_28 0.1610 4.8400e+06
; OA - P 600
;
#define gb_29 0.1630 4.7200e+06
; OA - SI 600
;
#define gb_30 0.1780 2.7200e+06
; FE - C (Heme)
;
#define gb_31 0.1780 5.9400e+06
; CH3 - S 900
;
#define gb_32 0.1830 5.6200e+06
; CH2 - S 900
;
#define gb_33 0.1870 3.5900e+06
; CH1 - SI 600
;
#define gb_34 0.198 0.6400e+06
; NR - FE 120
;
#define gb_35 0.200 0.6280e+06
; NR (heme) - FE 120
;
#define gb_36 0.2040 5.0300e+06
; S - S 1000
;
#define gb_37 0.221 0.5400e+06
; NR - FE 126
;
#define gb_38 0.1000 2.3200e+07
; HWat - OWat 1110
;
#define gb_39 0.1100 1.2100e+07
; HChl - CChl 700
;
#define gb_40 0.1758 8.1200e+06
; CChl - CLChl 1200
;
#define gb_41 0.1530 8.0400e+06
; ODmso - SDmso 900
;
#define gb_42 0.193799 4.9500e+06
; SDmso - CDmso 890
;
#define gb_43 0.1760 8.1000e+06
; CCl4 - CLCl4 1200
;
#define gb_44 0.1265 1.3100e+07
; CUrea - OUrea 1000
;
#define gb_45 0.135 1.0300e+07
; CUrea - NUrea 900
;
#define gb_46 0.163299 8.7100e+06
; HWat - HWat 1110
;
#define gb_47 0.233839 2.6800e+06
; HChl - CLChl 700
;
#define gb_48 0.290283 2.9800e+06
; CLChl - CLChl 1200
;
#define gb_49 0.279388 2.3900e+06
; ODmso - CDmso 890
;
#define gb_50 0.291189 2.1900e+06
; CDmso - CDmso 890
;
#define gb_51 0.2077 3.9700e+06
; HMet - CMet 820
;
#define gb_52 0.287407 3.0400e+06
; CLCl4 - CLCl4 1200
;
;---
; Table 2.5.3.1.
; GROMOS bond-angle bending parameters
;
;
; Bond-angle type code
; Force constant
; Ideal bond angle
; Example of usage in terms of non-bonded atom types
;
;
; ICT(H)[N] CT[N] (T0[N])
;
#define ga_1 90.00 380.00
; NR(heme) - FE - C 90
;
#define ga_2 90.00 420.00
; NR(heme) - FE - NR(heme) 100
;
#define ga_3 96.00 405.00
; H - S - CH2 95
;
#define ga_4 100.00 475.00
; CH2 - S - CH3 110
;
#define ga_5 103.00 420.00
; OA - P - OA 95
;
#define ga_6 104.00 490.00
; CH2 - S - S 110
;
#define ga_7 108.00 465.00
; NR, C, CR1(5-ring) 100
;
#define ga_8 109.50 285.00
; CHn - CHn - CHn, NR(6-ring) (sugar) 60
;
#define ga_9 109.50 320.00
; CHn, OA - CHn - OA, NR(ring) (sugar) 68
;
#define ga_10 109.50 380.00
; H - NL, NT - H, CHn - OA - CHn(sugar) 80
;
#define ga_11 109.50 425.00
; H - NL - C, CHn H - NT - CHn 90
;
#define ga_12 109.50 450.00
; X - OA, SI - X 95
;
#define ga_13 109.50 520.00
; CHn,C - CHn - C, CHn, OA, OM, N, NE 110
;
#define ga_14 109.60 450.00
; OM - P - OA 95
;
#define ga_15 111.00 530.00
; CHn - CHn - C, CHn, OA, NR, NT, NL 110
;
#define ga_16 113.00 545.00
; CHn - CH2 - S 110
;
#define ga_17 115.00 50.00
; NR(heme) - FE - NR 10
;
#define ga_18 115.00 460.00
; H - N - CHn 90
;
#define ga_19 115.00 610.00
; CHn, C - C - OA, N, NT, NL 120
;
#define ga_20 116.00 465.00
; H - NE - CH2 90
;
#define ga_21 116.00 620.00
; CH2 - N - CH1 120
;
#define ga_22 117.00 635.00
; CH3 - N - C, CHn - C - OM 120
;
#define ga_23 120.00 390.00
; H - NT, NZ, NE - C 70
;
#define ga_24 120.00 445.00
; H - NT, NZ - H 80
;
#define ga_25 120.00 505.00
; H - N - CH3, H, HC - 6-ring, H - NT - CHn 90
;
#define ga_26 120.00 530.00
; P, SI - OA - CHn, P 95
;
#define ga_27 120.00 560.00
; N, C, CR1 (6-ring, no H) 100
;
#define ga_28 120.00 670.00
; NZ - C - NZ, NE 120
;
#define ga_29 120.00 780.00
; OM - P - OM 140
;
#define ga_30 121.00 685.00
; O - C - CHn, C CH3 - N - CHn 120
;
#define ga_31 122.00 700.00
; CH1, CH2 - N - C 120
;
#define ga_32 123.00 415.00
; H - N - C 70
;
#define ga_33 124.00 730.00
; O - C - OA, N, NT, NL C - NE - CH2 120
;
#define ga_34 125.00 375.00
; FE - NR - CR1 (5-ring) 60
;
#define ga_35 125.00 750.00
; - 120
;
#define ga_36 126.00 575.00
; H, HC - 5-ring 90
;
#define ga_37 126.00 640.00
; X(noH) - 5-ring 100
;
#define ga_38 126.00 770.00
; OM - C - OM 120
;
#define ga_39 132.00 760.00
; 5, 6 ring connnection 100
;
#define ga_40 155.00 2215.00
; SI - OA - SI 95
;
#define ga_41 180.00 91350.00
; Fe - C - O (heme) 57
;
#define ga_42 109.50 434.00
; HWat - OWat - HWat 92
;
#define ga_43 107.57 484.00
; HChl - CChl - CLChl 105
;
#define ga_44 111.30 632.00
; CLChl - CChl - CLChl 131
;
#define ga_45 97.40 469.00
; CDmso - SDmso - CDmso 110
;
#define ga_46 106.75 503.00
; CDmso - SDmso - ODmso 110
;
#define ga_47 108.53 443.00
; HMet - OMet - CMet 95
;
#define ga_48 109.50 618.00
; CLCl4 - CCl4 - CLCl4 131
;
#define ga_49 107.60 507.00
; FTFE - CTFE - FTFE 100
;
#define ga_50 109.50 448.00
; HTFE - OTFE - CHTFE 85
;
#define ga_51 110.3 524.00
; OTFE - CHTFE - CTFE 97
;
#define ga_52 111.4 532.00
; CHTFE - CTFE - FTFE 95
;
#define ga_53 117.2 636.00
; NUrea - CUrea - NUrea 120
;
#define ga_54 121.4 690.00
; OUrea - CUrea - NUrea 120
;
; Table 2.5.4.1
; GROMOS improper (harmonic) dihedral angle parameters
;
;
; Improper dihedral-angle type code
; Force constant
; Ideal improper dihedral angle
; Example of usage
;
;
; ICQ(H)[N] CQ[N] (Q0[N])
;
#define gi_1 0.0 167.42309
; planar groups 40
;
#define gi_2 35.26439 334.84617
; tetrahedral centres 80
;
#define gi_3 0.0 669.69235
; heme iron 160
;
; Table 2.5.5.1 (Note: changes with respect to the 43A1 table)
; GROMOS (trigonometric) dihedral torsional angle parameters
;
;
; Dihedral-angle type code
; Force constant
; Phase shift
; Multiplicity
; Example of usage in terms of non-bonded atom types
;
;
; ICP(H)[N] CP[N] PD[N] NP[N]
;
#define gd_1 180.000 2.67 1
; CHn-CHn-CHn-OA (sugar) 0.6
;
#define gd_2 180.000 3.41 1
; OA-CHn-OA-CHn,H (beta sugar) 0.8
;
#define gd_3 180.000 4.97 1
; OA-CHn-CHn-OA (sugar) 1.2
;
#define gd_4 180.000 5.86 1
; N-CHn-CHn-OA (lipid) 1.4
;
#define gd_5 180.000 9.35 1
; OA-CHn-CHn-OA (sugar) 2.2
;
#define gd_6 180.000 9.45 1
; OA-CHn-OA-CHn,H (alpha sugar) 2.3
;
#define gd_7 0.000 2.79 1
; P-O5*-C5*-C4* (dna) 0.7
;
#define gd_8 0.000 5.35 1
; O5*-C5*-C4*-O4* (dna) 1.3
;
#define gd_9 180.000 1.53 2
; C1-C2-CAB-CBB (heme) 0.4
;
#define gd_10 180.000 5.86 2
; -C-C- 1.4
;
#define gd_11 180.000 7.11 2
; -C-OA,OE- (at ring) 1.7
;
#define gd_12 180.000 16.7 2
; -C-OA,OE- (carboxyl) 4.0
;
#define gd_13 180.000 24.0 2
; CHn-OE-C-CHn (ester lipid) 5.7
;
#define gd_14 180.000 33.5 2
; -C-N,NT,NE,NZ,NR- 8.0
;
#define gd_15 180.000 41.8 2
; -C-CR1- (6-ring) 10.0
;
#define gd_16 0.000 0.0 2
; -CH1(sugar)-NR(base) 0.0
;
#define gd_17 0.000 0.418 2
; O-CH1-CHn-no O 0.1
;
#define gd_18 0.000 2.09 2
; O-CH1-CHn-O 0.5
;
#define gd_19 0.000 3.14 2
; -OA-P- 0.75
;
#define gd_20 0.000 5.09 2
; O-P-O- (dna, lipids) 1.2
;
#define gd_21 0.000 16.7 2
; -S-S- 4.0
;
#define gd_22 0.000 1.05 3
; -OA-P- 0.25
;
#define gd_23 0.000 1.26 3
; -CHn-OA(no sugar)- 0.3
;
#define gd_24 0.000 1.30 3
; HTFE-OTFE-CHTFE-CTFE 0.3
;
#define gd_25 0.000 2.53 3
; O5*-C5*-C4*-O4* (dna) 0.6
;
#define gd_26 0.000 2.93 3
; -CH2-S- 0.7
;
#define gd_27 0.000 3.19 3
; O-P-O- (dna, lipids) 0.8
;
#define gd_28 0.000 3.65 3
; OA-CHn-OA-CHn,H (alpha sugar) 0.9
;
#define gd_29 0.000 3.77 3
; -C,CHn,SI- 0.9
;
#define gd_30 0.000 3.90 3
; CHn-CHn-OA-H (sugar) 0.9
;
#define gd_31 0.000 4.18 3
; HC-C-S- 1.0
;
#define gd_32 0.000 4.69 3
; AO-CHn-OA-CHn,H (beta sugar)
;
#define gd_33 0.000 5.44 3
; HC-C-C- 1.3
;
#define gd_34 0.000 5.92 3
; -CHn,SI-CHn- 1.4
;
#define gd_35 0.000 7.69 3
; OA-CHn-CHn-OA (sugar) 1.8
;
#define gd_36 0.000 8.62 3
; N-CHn-CHn-OA (lipid) 2.1
;
#define gd_37 0.000 9.50 3
; OA-CHn-CHn-OA (sugar) 2.3
;
#define gd_38 0.000 0.0 4
; -NR-FE- 0.0
;
#define gd_39 180.000 1.0 6
; -CHn-N,NE- 0.24
;
#define gd_40 0.000 1.0 6
; -CHn-C,NR(ring), CR1- 0.24
;
#define gd_41 0.000 3.77 6
; -CHn-NT- 0.9
;
; get the constraint distances for dummy atom constructions
#include "ff_dum.itp"
[ constrainttypes ]
; now the constraints for the rigid NH3 groups
MNH3 C 2 DC_MNC1
MNH3 CH1 2 DC_MNC2
MNH3 CH2 2 DC_MNC2
MNH3 MNH3 2 DC_MNMN
; and the angle-constraints for OH and SH groups in proteins:
CH2 H 2 DC_CO
CH1 H 2 DC_CO
C H 2 DC_CO
P H 2 DC_PO
; bond-, angle- and dihedraltypes for specbonds:
[ bondtypes ]
S S 2 gb_36
NR FE 2 gb_34
[ angletypes ]
CH1 CH2 S 2 ga_16
CH2 S S 2 ga_6
CR1 NR FE 2 ga_34
NR FE NR 2 ga_17
[ dihedraltypes ]
S S 1 gd_21
NR FE 1 gd_38
CH2 S 1 gd_26
|