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Add test for ibi_GBNO2/PTMA
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ricalessandri committed Aug 27, 2023
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338 changes: 338 additions & 0 deletions polyply/tests/test_data/library_tests/ibi_GBNO2/PTMA/polyply/PTMA.itp
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; /Users/alessandri/miniconda3/envs/polyplyRA/bin/polyply gen_params -lib ibi_GBNO2 -seq PTMA:10 -o PTMA.itp -name PTMA

; Please cite the following papers:
; Grunewald, F; Alessandri, R; Kroon, P C; Monticelli, L; Souza, P C; Marrink, S J; Nature Communications 2022; 10.1038/s41467-021-27627-4
; Alessandri, R; de Pablo, J J; Macromolecules 2023; 10.1021/acs.macromol.3c00141

[ moleculetype ]
PTMA 2

[ atoms ]
1 VNL 1 PTMA VNL 1 0.0 71.099
2 EST 1 PTMA EST 2 0.0 29.018
3 C1 1 PTMA C1 3 0.0 56.108
4 U 1 PTMA NN 4 0.0 0.0
5 U 1 PTMA OO 5 0.0 0.0
6 C1 1 PTMA C2 6 0.0 56.108
7 NO 1 PTMA NO 7 0.0 30.006
8 VNL 2 PTMA VNL 8 0.0 71.099
9 EST 2 PTMA EST 9 0.0 29.018
10 C1 2 PTMA C1 10 0.0 56.108
11 U 2 PTMA NN 11 0.0 0.0
12 U 2 PTMA OO 12 0.0 0.0
13 C1 2 PTMA C2 13 0.0 56.108
14 NO 2 PTMA NO 14 0.0 30.006
15 VNL 3 PTMA VNL 15 0.0 71.099
16 EST 3 PTMA EST 16 0.0 29.018
17 C1 3 PTMA C1 17 0.0 56.108
18 U 3 PTMA NN 18 0.0 0.0
19 U 3 PTMA OO 19 0.0 0.0
20 C1 3 PTMA C2 20 0.0 56.108
21 NO 3 PTMA NO 21 0.0 30.006
22 VNL 4 PTMA VNL 22 0.0 71.099
23 EST 4 PTMA EST 23 0.0 29.018
24 C1 4 PTMA C1 24 0.0 56.108
25 U 4 PTMA NN 25 0.0 0.0
26 U 4 PTMA OO 26 0.0 0.0
27 C1 4 PTMA C2 27 0.0 56.108
28 NO 4 PTMA NO 28 0.0 30.006
29 VNL 5 PTMA VNL 29 0.0 71.099
30 EST 5 PTMA EST 30 0.0 29.018
31 C1 5 PTMA C1 31 0.0 56.108
32 U 5 PTMA NN 32 0.0 0.0
33 U 5 PTMA OO 33 0.0 0.0
34 C1 5 PTMA C2 34 0.0 56.108
35 NO 5 PTMA NO 35 0.0 30.006
36 VNL 6 PTMA VNL 36 0.0 71.099
37 EST 6 PTMA EST 37 0.0 29.018
38 C1 6 PTMA C1 38 0.0 56.108
39 U 6 PTMA NN 39 0.0 0.0
40 U 6 PTMA OO 40 0.0 0.0
41 C1 6 PTMA C2 41 0.0 56.108
42 NO 6 PTMA NO 42 0.0 30.006
43 VNL 7 PTMA VNL 43 0.0 71.099
44 EST 7 PTMA EST 44 0.0 29.018
45 C1 7 PTMA C1 45 0.0 56.108
46 U 7 PTMA NN 46 0.0 0.0
47 U 7 PTMA OO 47 0.0 0.0
48 C1 7 PTMA C2 48 0.0 56.108
49 NO 7 PTMA NO 49 0.0 30.006
50 VNL 8 PTMA VNL 50 0.0 71.099
51 EST 8 PTMA EST 51 0.0 29.018
52 C1 8 PTMA C1 52 0.0 56.108
53 U 8 PTMA NN 53 0.0 0.0
54 U 8 PTMA OO 54 0.0 0.0
55 C1 8 PTMA C2 55 0.0 56.108
56 NO 8 PTMA NO 56 0.0 30.006
57 VNL 9 PTMA VNL 57 0.0 71.099
58 EST 9 PTMA EST 58 0.0 29.018
59 C1 9 PTMA C1 59 0.0 56.108
60 U 9 PTMA NN 60 0.0 0.0
61 U 9 PTMA OO 61 0.0 0.0
62 C1 9 PTMA C2 62 0.0 56.108
63 NO 9 PTMA NO 63 0.0 30.006
64 VNL 10 PTMA VNL 64 0.0 71.099
65 EST 10 PTMA EST 65 0.0 29.018
66 C1 10 PTMA C1 66 0.0 56.108
67 U 10 PTMA NN 67 0.0 0.0
68 U 10 PTMA OO 68 0.0 0.0
69 C1 10 PTMA C2 69 0.0 56.108
70 NO 10 PTMA NO 70 0.0 30.006

[ bonds ]
1 2 1 0.35337 12500
2 3 1 0.32325 32000
2 6 1 0.32369 32000
3 6 1 0.38838 32000
8 9 1 0.35337 12500
9 10 1 0.32325 32000
9 13 1 0.32369 32000
10 13 1 0.38838 32000
15 16 1 0.35337 12500
16 17 1 0.32325 32000
16 20 1 0.32369 32000
17 20 1 0.38838 32000
22 23 1 0.35337 12500
23 24 1 0.32325 32000
23 27 1 0.32369 32000
24 27 1 0.38838 32000
29 30 1 0.35337 12500
30 31 1 0.32325 32000
30 34 1 0.32369 32000
31 34 1 0.38838 32000
36 37 1 0.35337 12500
37 38 1 0.32325 32000
37 41 1 0.32369 32000
38 41 1 0.38838 32000
43 44 1 0.35337 12500
44 45 1 0.32325 32000
44 48 1 0.32369 32000
45 48 1 0.38838 32000
50 51 1 0.35337 12500
51 52 1 0.32325 32000
51 55 1 0.32369 32000
52 55 1 0.38838 32000
57 58 1 0.35337 12500
58 59 1 0.32325 32000
58 62 1 0.32369 32000
59 62 1 0.38838 32000
64 65 1 0.35337 12500
65 66 1 0.32325 32000
65 69 1 0.32369 32000
66 69 1 0.38838 32000

; vinyl backbone
1 8 1 0.305 12000
8 15 1 0.305 12000
15 22 1 0.305 12000
22 29 1 0.305 12000
29 36 1 0.305 12000
36 43 1 0.305 12000
43 50 1 0.305 12000
50 57 1 0.305 12000
57 64 1 0.305 12000

#ifdef FLEXIBLE
3 7 1 0.23794 1000000
6 7 1 0.23793 1000000
10 14 1 0.23794 1000000
13 14 1 0.23793 1000000
17 21 1 0.23794 1000000
20 21 1 0.23793 1000000
24 28 1 0.23794 1000000
27 28 1 0.23793 1000000
31 35 1 0.23794 1000000
34 35 1 0.23793 1000000
38 42 1 0.23794 1000000
41 42 1 0.23793 1000000
45 49 1 0.23794 1000000
48 49 1 0.23793 1000000
52 56 1 0.23794 1000000
55 56 1 0.23793 1000000
59 63 1 0.23794 1000000
62 63 1 0.23793 1000000
66 70 1 0.23794 1000000
69 70 1 0.23793 1000000
#endif

[ constraints ]
#ifndef FLEXIBLE
3 7 1 0.23794
6 7 1 0.23793
10 14 1 0.23794
13 14 1 0.23793
17 21 1 0.23794
20 21 1 0.23793
24 28 1 0.23794
27 28 1 0.23793
31 35 1 0.23794
34 35 1 0.23793
38 42 1 0.23794
41 42 1 0.23793
45 49 1 0.23794
48 49 1 0.23793
52 56 1 0.23794
55 56 1 0.23793
59 63 1 0.23794
62 63 1 0.23793
66 70 1 0.23794
69 70 1 0.23793
#endif

[ angles ]
1 2 3 2 130.000 90
1 2 6 2 130.000 75
8 9 10 2 130.000 90
8 9 13 2 130.000 75
15 16 17 2 130.000 90
15 16 20 2 130.000 75
22 23 24 2 130.000 90
22 23 27 2 130.000 75
29 30 31 2 130.000 90
29 30 34 2 130.000 75
36 37 38 2 130.000 90
36 37 41 2 130.000 75
43 44 45 2 130.000 90
43 44 48 2 130.000 75
50 51 52 2 130.000 90
50 51 55 2 130.000 75
57 58 59 2 130.000 90
57 58 62 2 130.000 75
64 65 66 2 130.000 90
64 65 69 2 130.000 75
2 1 8 2 90 20
9 8 15 2 90 20
16 15 22 2 90 20
23 22 29 2 90 20
30 29 36 2 90 20
37 36 43 2 90 20
44 43 50 2 90 20
51 50 57 2 90 20
58 57 64 2 90 20

; vinyl backbone
1 8 15 2 126 40
8 15 22 2 126 40
15 22 29 2 126 40
22 29 36 2 126 40
29 36 43 2 126 40
36 43 50 2 126 40
43 50 57 2 126 40
50 57 64 2 126 40

[ dihedrals ]
1 3 6 7 2 165.98 50
2 3 6 7 2 179.20 80
3 7 5 6 2 170.723 50
8 10 13 14 2 165.98 50
9 10 13 14 2 179.20 80
10 14 12 13 2 170.723 50
15 17 20 21 2 165.98 50
16 17 20 21 2 179.20 80
17 21 19 20 2 170.723 50
22 24 27 28 2 165.98 50
23 24 27 28 2 179.20 80
24 28 26 27 2 170.723 50
29 31 34 35 2 165.98 50
30 31 34 35 2 179.20 80
31 35 33 34 2 170.723 50
36 38 41 42 2 165.98 50
37 38 41 42 2 179.20 80
38 42 40 41 2 170.723 50
43 45 48 49 2 165.98 50
44 45 48 49 2 179.20 80
45 49 47 48 2 170.723 50
50 52 55 56 2 165.98 50
51 52 55 56 2 179.20 80
52 56 54 55 2 170.723 50
57 59 62 63 2 165.98 50
58 59 62 63 2 179.20 80
59 63 61 62 2 170.723 50
64 66 69 70 2 165.98 50
65 66 69 70 2 179.20 80
66 70 68 69 2 170.723 50

[ virtual_sites3 ]
4 3 2 7 2 0.834 0.210
5 3 2 7 2 1.180 0.276
11 10 9 14 2 0.834 0.210
12 10 9 14 2 1.180 0.276
18 17 16 21 2 0.834 0.210
19 17 16 21 2 1.180 0.276
25 24 23 28 2 0.834 0.210
26 24 23 28 2 1.180 0.276
32 31 30 35 2 0.834 0.210
33 31 30 35 2 1.180 0.276
39 38 37 42 2 0.834 0.210
40 38 37 42 2 1.180 0.276
46 45 44 49 2 0.834 0.210
47 45 44 49 2 1.180 0.276
53 52 51 56 2 0.834 0.210
54 52 51 56 2 1.180 0.276
60 59 58 63 2 0.834 0.210
61 59 58 63 2 1.180 0.276
67 66 65 70 2 0.834 0.210
68 66 65 70 2 1.180 0.276

[ exclusions ]
1 2 3 4 5 6 7
2 3 4 5 6 7
3 4 5 6 7
4 5 6 7
5 6 7
6 7
8 9 10 11 12 13 14
9 10 11 12 13 14
10 11 12 13 14
11 12 13 14
12 13 14
13 14
15 16 17 18 19 20 21
16 17 18 19 20 21
17 18 19 20 21
18 19 20 21
19 20 21
20 21
22 23 24 25 26 27 28
23 24 25 26 27 28
24 25 26 27 28
25 26 27 28
26 27 28
27 28
29 30 31 32 33 34 35
30 31 32 33 34 35
31 32 33 34 35
32 33 34 35
33 34 35
34 35
36 37 38 39 40 41 42
37 38 39 40 41 42
38 39 40 41 42
39 40 41 42
40 41 42
41 42
43 44 45 46 47 48 49
44 45 46 47 48 49
45 46 47 48 49
46 47 48 49
47 48 49
48 49
50 51 52 53 54 55 56
51 52 53 54 55 56
52 53 54 55 56
53 54 55 56
54 55 56
55 56
57 58 59 60 61 62 63
58 59 60 61 62 63
59 60 61 62 63
60 61 62 63
61 62 63
62 63
64 65 66 67 68 69 70
65 66 67 68 69 70
66 67 68 69 70
67 68 69 70
68 69 70
69 70

1 change: 1 addition & 0 deletions polyply/tests/test_data/library_tests/ibi_GBNO2/PTMA/polyply/command
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polyply gen_params -lib ibi_GBNO2 -seq PTMA:10 -o PTMA.itp -name PTMA
1 change: 1 addition & 0 deletions polyply/tests/test_lib_files.py
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Expand Up @@ -188,6 +188,7 @@ def _interaction_equal(interaction1, interaction2, inter_type):
['martini3', 'P3HT'],
['martini3', 'PPE'],
['martini3', 'PTMA'],
['ibi_GBNO2','PTMA'],
['martini2', 'PEO'],
['martini2', 'PS'],
['martini2', 'PEL'],
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