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changes to add tautomer functionality available.
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wiederm committed Apr 3, 2019
1 parent 79ce0da commit 008b3a3
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62 changes: 62 additions & 0 deletions examples/tautomers/bmi.json
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{

"_comment": "This script handles the calibration run for BMI (ligand of 2oj9).",
"name" : "bmi",
"input": {
"_comment": "Simulation requires an mmCIF file and a ffxml residue. Please specify the input directory under dir.",
"dir": "/home/mwieder/Work/Projects/protons-dev/protons/examples/tautomers/bmi/input/",
"structure": "bmi.cif"
},
"output": {
"dir": "/home/mwieder/Work/Projects/protons-dev/protons/examples/tautomers/bmi/output/"

},
"forcefield": {
"_comment1": "Standard, included xml files. Don't forget -obc2 files if using implicit.",
"default": ["amber10-constph.xml", "gaff.xml", "tip3p.xml"],
"_comment2": "Custom generated xml file (needs to be in input dir.",
"user": ["bmi.xml"]
},
"format_vars": {
"_comment1": "These variables are filled into file names for input and output when you use {} style syntax.",
"name": "bmi"
},
"system": {
"_comment1": "Systemwide settings, such as temperature, and long range method",
"_comment2": "If PME left out, nocutoff is used.",
"PME": {
"_comment": "Ewald + periodic system settings",
"ewald_error_tolerance": 1.0e-5,
"switching_distance_nm": 0.85,
"nonbonded_cutoff_nm": 1.0,
"barostat_interval": 25,
"pressure_atm": 1.0
},
"temperature_k": 300.0,
"salt_concentration_molar": 0.150
},
"integrator": {
"timestep_fs": 2.0,
"constraint_tolerance": 1.0e-7,
"collision_rate_per_ps": 1.0
},
"preprocessing": {
"minimization_tolerance_kjmol": 1.0e-5,
"minimization_max_iterations": 300,
"num_thermalization_steps": 100
},
"SAMS": {
"beta": 0.6,
"flatness_criterion": 0.1,
"sites": "multi",
"update_rule": "binary",
"min_burn": 200,
"min_slow": 200,
"min_fast": 200
},
"simulation" : {
"dcd_filename" : "{name}.dcd" ,
"netCDF4" : "{name}.nc"
}

}
221 changes: 221 additions & 0 deletions examples/tautomers/bmi/input/341660ed-06cd-4e0c-9a60-cf19422b7595-bondfix.mol2
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@<TRIPOS>MOLECULE
Structure5
49 53 0 0 0
SMALL
GASTEIGER

@<TRIPOS>ATOM
1 C1 3.6090 0.6174 -1.0694 C.ar 1 UNL1 0.2612
2 O1 4.2430 1.1446 -1.9825 O.2 1 UNL1 -0.2671
3 N1 0.0000 0.0000 0.0000 N.pl3 1 UNL1 -0.3375
4 N2 4.2256 0.0104 -0.0180 N.ar 1 UNL1 -0.3284
5 C2 1.4600 0.0000 0.0000 C.ar 1 UNL1 0.0448
6 C3 2.1963 -0.6286 1.0888 C.ar 1 UNL1 -0.0239
7 C4 3.5428 -0.5862 1.0154 C.ar 1 UNL1 0.0067
8 C5 -0.7300 -1.2644 0.0003 C.3 1 UNL1 0.0515
9 C6 -0.3124 -2.8932 -3.3965 C.ar 1 UNL1 -0.0586
10 C7 -0.0587 -2.5026 -2.0819 C.ar 1 UNL1 -0.0388
11 C8 -1.4876 -2.4654 -4.0105 C.ar 1 UNL1 -0.0436
12 C9 -0.9800 -1.6978 -1.4138 C.ar 1 UNL1 0.0582
13 N3 -2.1281 -1.2743 -2.0000 N.ar 1 UNL1 -0.2583
14 C10 -2.3628 -1.6620 -3.2808 C.ar 1 UNL1 0.0279
15 C11 2.1491 0.5849 -1.0130 C.ar 1 UNL1 0.1022
16 C12 -3.4790 2.6799 -6.3069 C.ar 1 UNL1 0.0293
17 C13 -1.1754 3.0676 -5.3133 C.ar 1 UNL1 0.0498
18 C14 -1.2589 2.3705 -4.1059 C.ar 1 UNL1 -0.0103
19 N4 -2.3988 3.4661 -6.0034 N.ar 1 UNL1 -0.3058
20 C15 -2.6948 4.7147 -6.4799 C.ar 1 UNL1 0.1004
21 N5 -3.8752 4.7586 -7.0542 N.ar 1 UNL1 -0.2437
22 C16 -4.3619 3.5300 -6.9560 C.ar 1 UNL1 0.0458
23 C17 -0.0730 1.9990 -3.4623 C.ar 1 UNL1 0.0917
24 N6 2.1001 1.8299 -3.1695 N.ar 1 UNL1 -0.3375
25 C18 1.4071 1.2367 -2.1420 C.ar 1 UNL1 0.1463
26 N7 0.1058 1.3180 -2.2829 N.ar 1 UNL1 -0.2274
27 C19 1.1720 2.3377 -4.0490 C.ar 1 UNL1 0.0695
28 C20 1.2633 3.0344 -5.2558 C.ar 1 UNL1 -0.0231
29 C21 0.0605 3.3904 -5.8723 C.ar 1 UNL1 -0.0328
30 C22 2.5855 3.3886 -5.8692 C.3 1 UNL1 -0.0376
31 H -0.5050 0.8747 0.0000 H 1 UNL1 0.1465
32 H 5.2340 0.0309 -0.0536 H 1 UNL1 0.1683
33 H 1.6865 -1.1065 1.9164 H 1 UNL1 0.0651
34 H 4.2081 -1.0140 1.7562 H 1 UNL1 0.0808
35 H -1.6824 -1.1340 0.5141 H 1 UNL1 0.0526
36 H -0.1409 -2.0239 0.5143 H 1 UNL1 0.0526
37 H 0.3912 -3.5176 -3.9304 H 1 UNL1 0.0619
38 H 0.8462 -2.8212 -1.5828 H 1 UNL1 0.0636
39 H -1.7169 -2.7490 -5.0286 H 1 UNL1 0.0633
40 H -3.2841 -1.3150 -3.7334 H 1 UNL1 0.0829
41 H -3.5216 1.6294 -6.0449 H 1 UNL1 0.0829
42 H -2.2176 2.1216 -3.6747 H 1 UNL1 0.0660
43 H -1.9881 5.5298 -6.3621 H 1 UNL1 0.1032
44 H -5.3359 3.2588 -7.3473 H 1 UNL1 0.0845
45 H 3.1139 1.8582 -3.2185 H 1 UNL1 0.1674
46 H 0.0865 3.9316 -6.8098 H 1 UNL1 0.0641
47 H 2.4205 3.9273 -6.8023 H 1 UNL1 0.0278
48 H 3.1484 4.0187 -5.1806 H 1 UNL1 0.0278
49 H 3.1484 2.4772 -6.0706 H 1 UNL1 0.0278
@<TRIPOS>BOND
1 1 2 2
2 1 4 1
3 1 15 1
4 3 5 1
5 3 8 1
6 3 31 1
7 4 7 1
8 4 32 1
9 5 6 1
10 5 15 2
11 6 7 2
12 6 33 1
13 7 34 1
14 8 12 1
15 8 35 1
16 8 36 1
17 9 10 2
18 9 11 1
19 9 37 1
20 10 12 1
21 10 38 1
22 11 14 2
23 11 39 1
24 12 13 2
25 13 14 1
26 14 40 1
27 15 25 1
28 16 19 1
29 16 22 2
30 16 41 1
31 17 18 1
32 17 19 1
33 17 29 2
34 18 23 1
35 18 42 1
36 19 20 1
37 20 21 2
38 20 43 1
39 21 22 1
40 22 44 1
41 23 26 2
42 23 27 1
43 24 25 2
44 24 27 1
45 24 45 1
46 25 26 1
47 27 28 2
48 28 29 1
49 28 30 1
50 29 46 1
51 30 47 1
52 30 48 1
53 30 49 1

@<TRIPOS>MOLECULE
Structure6
49 53 0 0 0
SMALL
GASTEIGER

@<TRIPOS>ATOM
1 C1 3.6090 0.6174 -1.0694 C.ar 1 UNL1 0.2612
2 O1 4.2430 1.1446 -1.9825 O.2 1 UNL1 -0.2671
3 N1 0.0000 0.0000 0.0000 N.pl3 1 UNL1 -0.3375
4 N2 4.2256 0.0104 -0.0180 N.ar 1 UNL1 -0.3284
5 C2 1.4600 0.0000 0.0000 C.ar 1 UNL1 0.0448
6 C3 2.1963 -0.6286 1.0888 C.ar 1 UNL1 -0.0239
7 C4 3.5428 -0.5862 1.0154 C.ar 1 UNL1 0.0067
8 C5 -0.7300 -1.2644 0.0003 C.3 1 UNL1 0.0515
9 C6 -0.3124 -2.8932 -3.3965 C.ar 1 UNL1 -0.0586
10 C7 -0.0587 -2.5026 -2.0819 C.ar 1 UNL1 -0.0388
11 C8 -1.4876 -2.4654 -4.0105 C.ar 1 UNL1 -0.0436
12 C9 -0.9800 -1.6978 -1.4138 C.ar 1 UNL1 0.0582
13 N3 -2.1281 -1.2743 -2.0000 N.ar 1 UNL1 -0.2583
14 C10 -2.3628 -1.6620 -3.2808 C.ar 1 UNL1 0.0279
15 C11 2.1491 0.5849 -1.0130 C.ar 1 UNL1 0.1022
16 C12 0.8141 5.2498 -7.4277 C.ar 1 UNL1 0.0293
17 C13 0.0605 3.3904 -5.8723 C.ar 1 UNL1 0.0498
18 C14 1.2633 3.0344 -5.2558 C.ar 1 UNL1 -0.0123
19 N4 0.0956 4.1202 -7.1364 N.ar 1 UNL1 -0.3058
20 C15 -0.5921 3.8054 -8.2773 C.ar 1 UNL1 0.1004
21 N5 -0.3526 4.6548 -9.2502 N.ar 1 UNL1 -0.2437
22 C16 0.4995 5.5366 -8.7477 C.ar 1 UNL1 0.0458
23 C17 1.1720 2.3377 -4.0490 C.ar 1 UNL1 0.0687
24 N6 0.1058 1.3180 -2.2829 N.ar 1 UNL1 -0.2272
25 C18 1.4071 1.2367 -2.1420 C.ar 1 UNL1 0.1463
26 N7 2.1001 1.8299 -3.1695 N.ar 1 UNL1 -0.3376
27 C19 -0.0730 1.9990 -3.4623 C.ar 1 UNL1 0.0925
28 C20 -1.2589 2.3705 -4.1059 C.ar 1 UNL1 -0.0211
29 C21 -1.1754 3.0676 -5.3133 C.ar 1 UNL1 -0.0328
30 C22 -2.5901 2.0249 -3.5073 C.3 1 UNL1 -0.0376
31 H -0.5050 0.8747 0.0000 H 1 UNL1 0.1465
32 H 5.2340 0.0309 -0.0536 H 1 UNL1 0.1683
33 H 1.6865 -1.1065 1.9164 H 1 UNL1 0.0651
34 H 4.2081 -1.0140 1.7562 H 1 UNL1 0.0808
35 H -1.6824 -1.1340 0.5141 H 1 UNL1 0.0526
36 H -0.1409 -2.0239 0.5143 H 1 UNL1 0.0526
37 H 0.3912 -3.5176 -3.9304 H 1 UNL1 0.0619
38 H 0.8462 -2.8212 -1.5828 H 1 UNL1 0.0636
39 H -1.7169 -2.7490 -5.0286 H 1 UNL1 0.0633
40 H -3.2841 -1.3150 -3.7334 H 1 UNL1 0.0829
41 H 1.4583 5.7290 -6.7003 H 1 UNL1 0.0829
42 H 2.2166 3.2898 -5.6981 H 1 UNL1 0.0659
43 H -1.2438 2.9382 -8.3047 H 1 UNL1 0.1032
44 H 0.8829 6.3685 -9.3275 H 1 UNL1 0.0845
45 H 3.1139 1.8582 -3.2185 H 1 UNL1 0.1674
46 H -2.0826 3.3631 -5.8250 H 1 UNL1 0.0641
47 H -3.3861 2.3972 -4.1521 H 1 UNL1 0.0278
48 H -2.6758 0.9424 -3.4123 H 1 UNL1 0.0278
49 H -2.6758 2.4839 -2.5223 H 1 UNL1 0.0278
@<TRIPOS>BOND
1 1 2 2
2 1 4 1
3 1 15 1
4 3 5 1
5 3 8 1
6 3 31 1
7 4 7 1
8 4 32 1
9 5 6 1
10 5 15 2
11 6 7 2
12 6 33 1
13 7 34 1
14 8 12 1
15 8 35 1
16 8 36 1
17 9 10 2
18 9 11 1
19 9 37 1
20 10 12 1
21 10 38 1
22 11 14 2
23 11 39 1
24 12 13 2
25 13 14 1
26 14 40 1
27 15 25 1
28 16 19 1
29 16 22 2
30 16 41 1
31 17 18 1
32 17 19 1
33 17 29 2
34 18 23 1
35 18 42 1
36 19 20 1
37 20 21 2
38 20 43 1
39 21 22 1
40 22 44 1
41 23 26 2
42 23 27 1
43 24 25 2
44 24 27 1
45 25 26 1
46 26 45 1
47 27 28 2
48 28 29 1
49 28 30 1
50 29 46 1
51 30 47 1
52 30 48 1
53 30 49 1
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