From e9fe4c16d4c8d552418c19e7ffe4225b58f994db Mon Sep 17 00:00:00 2001 From: csbrasnett Date: Thu, 10 Oct 2024 09:43:43 +0200 Subject: [PATCH] added integration test for complex histidine modifications: - 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. --- .../martini3/PROTMODS/polyply/HIS5_mods.itp | 169 ++++++++++++++++++ .../martini3/PROTMODS/polyply/command | 1 + 2 files changed, 170 insertions(+) create mode 100644 polyply/tests/test_data/library_tests/martini3/PROTMODS/polyply/HIS5_mods.itp create mode 100644 polyply/tests/test_data/library_tests/martini3/PROTMODS/polyply/command diff --git a/polyply/tests/test_data/library_tests/martini3/PROTMODS/polyply/HIS5_mods.itp b/polyply/tests/test_data/library_tests/martini3/PROTMODS/polyply/HIS5_mods.itp new file mode 100644 index 00000000..41617da6 --- /dev/null +++ b/polyply/tests/test_data/library_tests/martini3/PROTMODS/polyply/HIS5_mods.itp @@ -0,0 +1,169 @@ +; 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 + diff --git a/polyply/tests/test_data/library_tests/martini3/PROTMODS/polyply/command b/polyply/tests/test_data/library_tests/martini3/PROTMODS/polyply/command new file mode 100644 index 00000000..cfa99208 --- /dev/null +++ b/polyply/tests/test_data/library_tests/martini3/PROTMODS/polyply/command @@ -0,0 +1 @@ +polyply gen_params -lib martini3 -seq HIS:5 -name HIS5_mods -o HIS5_mods.itp -mods HIS1:HIS-HD HIS1:NH2-ter \ No newline at end of file