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added integration test for complex histidine modifications:
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- input -seq HIS:5
- with two modifications, HIS1:HIS-HD HIS1:NH2-ter, so the first residue is modified twice, both in its terminal type, and in its histidine variant.
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csbrasnett committed Oct 10, 2024
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169 changes: 169 additions & 0 deletions polyply/tests/test_data/library_tests/martini3/PROTMODS/polyply/HIS5_mods.itp
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; Please cite the following papers:
; Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3
; Souza, P C T; Araujo, L P B; Brasnett, C; Moreira, R A; Grunewald, F; Park, P; Wang, L; Razmazma, H; Borges-Araujo, A C; Cofas-Vargas, L F; Monticelli, L; Mera-Adasme, R; Melo, M N; Wu, S; Marrink, S J; Poma, A B; Thallmair, S; 2024; 10.1101/2024.04.15.589479
; Grunewald, F; Alessandri, R; Kroon, P C; Monticelli, L; Souza, P C; Marrink, S J; Nature Communications 2022; 10.1038/s41467-021-27627-4

[ moleculetype ]
HIS5_mods 1

[ atoms ]
1 P6 1 HIS BB 1 0.0
2 TC4 1 HIS SC1 1 0.0
3 TN5a 1 HIS SC2 1 0.0
4 TN6a 1 HIS SC3 1 0.0
5 VS 1 HIS CA 1 0.0 0.0
6 P2 2 HIS BB 2 0.0
7 TC4 2 HIS SC1 2 0.0
8 TN6d 2 HIS SC2 2 0.0
9 TN5a 2 HIS SC3 2 0.0
10 VS 2 HIS CA 2 0.0 0.0
11 P2 3 HIS BB 3 0.0
12 TC4 3 HIS SC1 3 0.0
13 TN6d 3 HIS SC2 3 0.0
14 TN5a 3 HIS SC3 3 0.0
15 VS 3 HIS CA 3 0.0 0.0
16 P2 4 HIS BB 4 0.0
17 TC4 4 HIS SC1 4 0.0
18 TN6d 4 HIS SC2 4 0.0
19 TN5a 4 HIS SC3 4 0.0
20 VS 4 HIS CA 4 0.0 0.0
21 Q5 5 HIS BB 5 -1.0
22 TC4 5 HIS SC1 5 0.0
23 TN6d 5 HIS SC2 5 0.0
24 TN5a 5 HIS SC3 5 0.0
25 VS 5 HIS CA 5 0.0 0.0

[ position_restraints ]
#ifdef POSRES
1 1 1000 1000 1000
6 1 1000 1000 1000
11 1 1000 1000 1000
16 1 1000 1000 1000
21 1 1000 1000 1000
#endif

[ bonds ]
; Backbone bonds
1 6 1 0.350 4000
6 11 1 0.350 4000
11 16 1 0.350 4000
16 21 1 0.350 4000

; Side chain bonds
1 2 1 0.336 7500
6 7 1 0.336 7500
11 12 1 0.336 7500
16 17 1 0.336 7500
21 22 1 0.336 7500

#ifdef FLEXIBLE
; Side chain bonds
2 3 1 0.320 1000000
2 4 1 0.300 1000000
3 4 1 0.270 1000000
7 8 1 0.320 1000000
7 9 1 0.300 1000000
8 9 1 0.270 1000000
12 13 1 0.320 1000000
12 14 1 0.300 1000000
13 14 1 0.270 1000000
17 18 1 0.320 1000000
17 19 1 0.300 1000000
18 19 1 0.270 1000000
22 23 1 0.320 1000000
22 24 1 0.300 1000000
23 24 1 0.270 1000000
#endif

[ constraints ]
#ifndef FLEXIBLE
; Side chain bonds
2 3 1 0.320
2 4 1 0.300
3 4 1 0.270
7 8 1 0.320
7 9 1 0.300
8 9 1 0.270
12 13 1 0.320
12 14 1 0.300
13 14 1 0.270
17 18 1 0.320
17 19 1 0.300
18 19 1 0.270
22 23 1 0.320
22 24 1 0.300
23 24 1 0.270
#endif

[ virtual_sitesn ]
5 1 1
10 1 6
15 1 11
20 1 16
25 1 21

[ angles ]
; BBB angles
1 6 11 10 127 20
6 11 16 10 127 20
11 16 21 10 127 20

; Side chain angles
1 2 3 2 120.000 50.0
1 2 4 2 120.000 50.0
6 7 8 2 120.000 50.0
6 7 9 2 120.000 50.0
11 12 13 2 120.000 50.0
11 12 14 2 120.000 50.0
16 17 18 2 120.000 50.0
16 17 19 2 120.000 50.0
21 22 23 2 120.000 50.0
21 22 24 2 120.000 50.0

; idp-fix
1 6 7 10 85 10
6 11 12 10 85 10
11 16 17 10 85 10
16 21 22 10 85 10
2 1 6 10 85 10
7 6 11 10 85 10
12 11 16 10 85 10
17 16 21 10 85 10

[ dihedrals ]
; idp-fix
1 6 11 16 9 -120 -1 1 ; BB-BB-BB-BB-v1
1 6 11 16 9 -120 -1 2 ; BB-BB-BB-BB-v2
6 11 16 21 9 -120 -1 1 ; BB-BB-BB-BB-v1
6 11 16 21 9 -120 -1 2 ; BB-BB-BB-BB-v2
2 1 6 7 9 -130 -1.5 1 ; SC1-BB-BB-SC1-v1
2 1 6 7 9 100 -1.5 2 ; SC1-BB-BB-SC1-v2
7 6 11 12 9 -130 -1.5 1 ; SC1-BB-BB-SC1-v1
7 6 11 12 9 100 -1.5 2 ; SC1-BB-BB-SC1-v2
12 11 16 17 9 -130 -1.5 1 ; SC1-BB-BB-SC1-v1
12 11 16 17 9 100 -1.5 2 ; SC1-BB-BB-SC1-v2
17 16 21 22 9 -130 -1.5 1 ; SC1-BB-BB-SC1-v1
17 16 21 22 9 100 -1.5 2 ; SC1-BB-BB-SC1-v2

[ exclusions ]
1 2 3 4
2 3 4
3 4
6 7 8 9
7 8 9
8 9
11 12 13 14
12 13 14
13 14
16 17 18 19
17 18 19
18 19
21 22 23 24
22 23 24
23 24
5 1 ; CA-BB-same
10 6 ; CA-BB-same
15 11 ; CA-BB-same
20 16 ; CA-BB-same
25 21 ; CA-BB-same

1 change: 1 addition & 0 deletions polyply/tests/test_data/library_tests/martini3/PROTMODS/polyply/command
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polyply gen_params -lib martini3 -seq HIS:5 -name HIS5_mods -o HIS5_mods.itp -mods HIS1:HIS-HD HIS1:NH2-ter

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