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GM1-GM2.itp
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289 lines (270 loc) · 7.01 KB
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; Martini 3 models for monosialotetrahexosylganglioside and
; monosialotrihexosylganglioside gangliosides (aka GM1 and GM2),
; developed by Martín Calvelo and Manuel N. Melo.
; (m.calvelo@itqb.unl.pt, m.n.melo@itqb.unl.pt)
;
; Based on the GM3 ganglioside model released with the Martini 3 carbohydrate
; parameterization (Grünewald et al., 2022, doi:10.1021/acs.jctc.2c00757).
;; GM1
[ moleculetype ]
GM1 1
[ atoms ]
1 SP1r 1 GM1 A2 1 0.0 54.0
2 SP1r 1 GM1 B2 2 0.0 54.0
3 SP1r 1 GM1 C2 3 0.0 54.0
4 TC4 1 GM1 V2 4 0.0 0.0
5 SN6 1 GM1 A3 5 0.0 54.0
6 SN4ar 1 GM1 B3 6 0.0 54.0
7 SP1r 1 GM1 C3 7 0.0 54.0
8 TC4 1 GM1 V3 8 0.0 0.0
9 Q5n 1 GM1 A4 9 -1.0 72.0
10 SN6 1 GM1 B4 10 0.0 54.0
11 SP1r 1 GM1 C4 11 0.0 54.0
12 SP3d 1 GM1 D4 12 0.0 54.0
13 SP3 1 GM1 E4 13 0.0 54.0
14 TC4 1 GM1 V4 14 0.0 0.0
15 SN4ar 1 GM1 A5 15 0.0 54.0
16 SP1r 1 GM1 B5 16 0.0 54.0
17 SP1r 1 GM1 C5 17 0.0 54.0
18 SP3d 1 GM1 D5 18 0.0 54.0
19 TC4 1 GM1 V5 19 0.0 0.0
20 SN6 1 GM1 A6 20 0.0 54.0
21 SP4r 1 GM1 B6 21 0.0 54.0
22 SP1r 1 GM1 C6 22 0.0 54.0
23 TC4 1 GM1 V6 23 0.0 0.0
24 SP1 1 GM1 AM1 24 0.0 54.0
25 SP2 1 GM1 AM2 25 0.0 54.0
26 C4h 1 GM1 T1A 26 0.0 54.0
27 C1 1 GM1 C2A 27 0.0 54.0
28 C1 1 GM1 C3A 28 0.0 54.0
29 C1 1 GM1 C1B 29 0.0 54.0
30 C1 1 GM1 C2B 30 0.0 54.0
31 C1 1 GM1 C3B 31 0.0 54.0
32 C1 1 GM1 C4B 32 0.0 54.0
[ bonds ]
; glycosidic bonds
2 5 1 0.3800 6000
6 9 1 0.3250 17000
6 15 1 0.3230 17000
16 20 1 0.3780 7000
10 12 1 0.3600 7000
11 13 1 0.2990 7000
15 18 1 0.3450 18500
; tails
1 24 1 0.36 6000
24 25 1 0.35 8000
24 26 1 0.47 5000
26 27 1 0.47 3800
27 28 1 0.47 3800
25 29 1 0.47 5000
29 30 1 0.47 3800
30 31 1 0.47 3800
31 32 1 0.47 3800
[ constraints ]
; intra-ring constraints
; increased by +15% relative to AA reference distances
1 2 1 0.344
1 3 1 0.491
2 3 1 0.397
5 6 1 0.298
5 7 1 0.492
6 7 1 0.396
9 10 1 0.322
9 11 1 0.449
10 11 1 0.384
15 16 1 0.346
15 17 1 0.437
16 17 1 0.378
20 21 1 0.327
20 22 1 0.494
21 22 1 0.401
[ angles ]
; glycosidic bond bending
; ring 2--3
3 2 5 2 55 125
2 5 7 2 68 240
; ring 3--4
5 6 9 10 103 175
6 9 11 10 67 60
; ring 3--5
7 6 15 2 81 325
6 15 17 10 110 170
; ring 5--6
15 16 20 10 100 170
16 20 22 10 76 90
; sugar substituents
11 10 12 10 62 95
9 11 13 10 122 95
16 15 18 2 101 250
; tails
2 1 24 10 153 260
3 1 24 2 97 200
1 24 25 2 134 150
1 24 26 10 143 90
24 25 29 2 129 200
24 26 27 2 180 35
26 27 28 2 180 35
25 29 30 2 180 35
29 30 31 2 180 35
30 31 32 2 180 35
[ dihedrals ]
; glycosidic bond torsions
; ring 2--3
5 2 3 1 2 -165 65
2 5 7 6 2 180 80
3 2 5 7 2 -140 10
; ring 3--4
9 6 5 7 2 -170 105
6 9 11 10 2 130 80
5 6 9 11 9 110 0.5 1
5 6 9 11 9 -170 4.5 2
5 6 9 11 9 100 4.2 3
5 6 9 11 9 -55 2.8 4
; ring 3--5
15 6 7 5 2 107 150
6 15 17 16 2 160 100
7 6 15 17 2 69 70
; ring 5--6
20 16 15 17 2 180 45
16 20 22 21 2 -154 90
15 16 20 22 2 -140 10
; sugar substituents
9 11 10 12 2 140 75
13 11 9 10 2 150 25
18 15 16 17 2 -178 50
[ virtual_sitesn ]
; ring-center beads
4 1 1 2 3
8 1 5 6 7
14 1 9 10 11
19 1 15 16 17
23 1 20 21 22
[ exclusions ]
4 1 2 3
8 5 6 7
14 9 10 11 12 13
19 15 16 17 18
23 20 21 22
;; GM2
[ moleculetype ]
GM2 1
[ atoms ]
1 SP1r 2 GM2 A2 1 0.0 54.0
2 SP1r 2 GM2 B2 2 0.0 54.0
3 SP1r 2 GM2 C2 3 0.0 54.0
4 TC4 2 GM2 V2 4 0.0 0.0
5 SN6 3 GM2 A3 5 0.0 54.0
6 SN4ar 3 GM2 B3 6 0.0 54.0
7 SP1r 3 GM2 C3 7 0.0 54.0
8 TC4 3 GM2 V3 8 0.0 0.0
9 Q5n 4 GM2 A4 9 -1.0 72.0
10 SN6 4 GM2 B4 10 0.0 54.0
11 SP1r 4 GM2 C4 11 0.0 54.0
12 SP3d 4 GM2 D4 12 0.0 54.0
13 SP3 4 GM2 E4 13 0.0 54.0
14 TC4 4 GM2 V4 14 0.0 0.0
15 SN4ar 5 GM2 A5 15 0.0 54.0
16 SP4r 5 GM2 B5 16 0.0 54.0
17 SP1r 5 GM2 C5 17 0.0 54.0
18 SP3d 5 GM2 D5 18 0.0 54.0
19 TC4 5 GM2 V5 19 0.0 0.0
20 SP1 1 GM2 AM1 20 0.0 54.0
21 SP2 1 GM2 AM2 21 0.0 54.0
22 C4h 1 GM2 T1A 22 0.0 54.0
23 C1 1 GM2 C2A 23 0.0 54.0
24 C1 1 GM2 C3A 24 0.0 54.0
25 C1 1 GM2 C1B 25 0.0 54.0
26 C1 1 GM2 C2B 26 0.0 54.0
27 C1 1 GM2 C3B 27 0.0 54.0
28 C1 1 GM2 C4B 28 0.0 54.0
[ bonds ]
; glycosidic bonds
2 5 1 0.3800 6000
6 9 1 0.3250 17000
6 15 1 0.3230 17000
10 12 1 0.3600 7000
11 13 1 0.2990 7000
15 18 1 0.3450 18500
; tails
1 20 1 0.36 6000
20 21 1 0.35 8000
20 22 1 0.47 5000
22 23 1 0.47 3800
23 24 1 0.47 3800
21 25 1 0.47 5000
25 26 1 0.47 3800
26 27 1 0.47 3800
27 28 1 0.47 3800
[ constraints ]
; intra-ring constraints
; increased by +15% relative to AA reference distances
1 2 1 0.344
1 3 1 0.491
2 3 1 0.397
5 6 1 0.298
5 7 1 0.492
6 7 1 0.396
9 10 1 0.322
9 11 1 0.449
10 11 1 0.384
15 16 1 0.346
15 17 1 0.437
16 17 1 0.378
[ angles ]
; glycosidic bond bending
; ring 2--3
3 2 5 2 55 125
2 5 7 2 68 240
; ring 3--4
5 6 9 10 103 175
6 9 11 10 67 60
; ring 3--5
7 6 15 2 81 325
6 15 17 10 110 170
; sugar substituents
11 10 12 10 62 95
9 11 13 10 122 95
16 15 18 2 101 250
; tails
2 1 20 10 153 260
3 1 20 2 97 200
1 20 21 2 134 150
1 20 22 10 143 90
20 21 25 2 129 200
20 22 23 2 180 35
22 23 24 2 180 35
21 25 26 2 180 35
25 26 27 2 180 35
26 27 28 2 180 35
[ dihedrals ]
; glycosidic bond torsions
; ring 2--3
5 2 3 1 2 -165 65
2 5 7 6 2 180 80
3 2 5 7 2 -140 10
; ring 3--4
9 6 5 7 2 -170 105
6 9 11 10 2 130 80
5 6 9 11 9 110 0.5 1
5 6 9 11 9 -170 4.5 2
5 6 9 11 9 100 4.2 3
5 6 9 11 9 -55 2.8 4
; ring 3--5
15 6 7 5 2 107 150
6 15 17 16 2 160 100
7 6 15 17 2 69 70
; sugar substituents
9 11 10 12 2 140 75
13 11 9 10 2 150 25
18 15 16 17 2 -178 50
[ virtual_sitesn ]
; ring-center beads
4 1 1 2 3
8 1 5 6 7
14 1 9 10 11
19 1 15 16 17
[ exclusions ]
4 1 2 3
8 5 6 7
14 9 10 11 12 13
19 15 16 17 18