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checkpoint: before switching to dev after git pull origin master
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@e-mayo
e-mayo committed Aug 9, 2021
1 parent f2e9c55 commit 8cc4935
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74 changes: 74 additions & 0 deletions data/config_dock_sample.txt
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conformer_search_type flex
write_fragment_libraries no
user_specified_anchor no
limit_max_anchors no
min_anchor_size 5
pruning_use_clustering yes
pruning_max_orients 1000
pruning_clustering_cutoff 100
pruning_conformer_score_cutoff 100.0
pruning_conformer_score_scaling_factor 1.0
use_clash_overlap no
write_growth_tree no
use_internal_energy yes
internal_energy_rep_exp 12
internal_energy_cutoff 100.0
ligand_atom_file dock_structures/out_folder/here/lig_3ebh.mol2
limit_max_ligands no
skip_molecule no
read_mol_solvation no
calculate_rmsd no
use_database_filter no
orient_ligand yes
automated_matching yes
receptor_site_file dock_structures/out_folder/here/frag-rec_3ebh-sele.sph
max_orientations 1000
critical_points no
chemical_matching no
use_ligand_spheres no
bump_filter no
score_molecules yes
contact_score_primary no
contact_score_secondary no
grid_score_primary yes
grid_score_secondary no
grid_score_rep_rad_scale 1
grid_score_vdw_scale 1
grid_score_es_scale 1
grid_score_grid_prefix dock_structures/out_folder/here/rec_3ebh-grid
multigrid_score_secondary no
dock3.5_score_secondary no
continuous_score_secondary no
footprint_similarity_score_secondary no
pharmacophore_score_secondary no
descriptor_score_secondary no
gbsa_zou_score_secondary no
gbsa_hawkins_score_secondary no
SASA_score_secondary no
amber_score_secondary no
minimize_ligand yes
minimize_anchor yes
minimize_flexible_growth yes
use_advanced_simplex_parameters no
simplex_max_cycles 1
simplex_score_converge 0.1
simplex_cycle_converge 1.0
simplex_trans_step 1.0
simplex_rot_step 0.1
simplex_tors_step 10.0
simplex_anchor_max_iterations 500
simplex_grow_max_iterations 500
simplex_grow_tors_premin_iterations 0
simplex_random_seed 0
simplex_restraint_min no
atom_model all
vdw_defn_file /home/edd/dock6/parameters/vdw_AMBER_parm99.defn
flex_defn_file /home/edd/dock6/parameters/flex.defn
flex_drive_file /home/edd/dock6/parameters/flex_drive.tbl
ligand_outfile_prefix dock_structures/out_folder/dock_out/rec_3ebh-flex-out
write_orientations yes
num_scored_conformers 25
write_conformations yes
cluster_conformations yes
cluster_rmsd_threshold 2
rank_ligands no
18 changes: 18 additions & 0 deletions data/config_ledock_sample.in
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Receptor
pro.pdb

RMSD
1.0

Binding pocket
45.3 62.6
-25.9 -12.9
29.7 47.1

Number of binding poses
20

Ligands list
ligand.list

END
6 changes: 6 additions & 0 deletions data/config_plants_speed4.txt
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search_speed speed4
bindingsite_center 53.96 -19.14 38.39
bindingsite_radius 13.77
cluster_rmsd 2.0
cluster_structures 10
output_dir /folder/out
10 changes: 10 additions & 0 deletions data/config_vina_ex1.txt
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center_x = 54.0
center_y = -19.1
center_z = 38.4
size_x = 17.3
size_y = 12.4
size_z = 17.4
exhaustiveness = 1
num_modes = 10


9 changes: 9 additions & 0 deletions data/config_vina_ex2.txt
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center_x = 62.467
center_y = 4.815
center_z = -32.164
size_x = 40
size_y = 40
size_z = 40
exhaustiveness = 2
num_modes = 10

110 changes: 110 additions & 0 deletions data/ligands/lig_3ebh.mol2
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@<TRIPOS>MOLECULE
pdb3ebh.ent_out_ok
46 46 2
SMALL
GASTEIGER

@<TRIPOS>DICT

@<TRIPOS>ATOM
1 C 12.6320 12.0820 12.4700 C.3 0 UNK0 0.0000
2 C 13.4180 12.2750 11.1510 C.3 0 UNK0 0.0000
3 N 11.3380 12.7770 12.4720 N.4 0 UNK0 1.0000
4 O 12.5430 12.5120 10.0700 O.3 0 UNK0 0.0000
5 C 14.2020 11.0080 10.8320 C.2 0 UNK0 0.0000
6 O 13.5950 10.0060 10.4860 O.2 0 UNK0 0.0000
7 C 13.4950 12.4790 13.6740 C.3 0 UNK0 0.0000
8 C 13.0550 11.8350 14.9690 C.ar 0 UNK0 0.0000
9 C 12.2090 12.5230 15.8580 C.ar 0 UNK0 0.0000
10 C 11.8480 11.9320 17.0820 C.ar 0 UNK0 0.0000
11 C 12.3420 10.6610 17.4250 C.ar 0 UNK0 0.0000
12 C 13.1790 9.9650 16.5320 C.ar 0 UNK0 0.0000
13 C 13.5270 10.5470 15.2990 C.ar 0 UNK0 0.0000
14 H 13.0490 12.8240 9.3400 H 0 UNK0 0.0000
15 H 12.3680 11.0320 12.5840 H 0 UNK0 0.0000
16 H 14.0750 13.1420 11.2290 H 0 UNK0 0.0000
17 H 11.8450 13.5060 15.5980 H 0 UNK0 0.0000
18 H 11.1880 12.4480 17.7590 H 0 UNK0 0.0000
19 H 12.0650 10.2100 18.3670 H 0 UNK0 0.0000
20 H 13.5490 8.9850 16.7880 H 0 UNK0 0.0000
21 H 14.1750 10.0130 14.6220 H 0 UNK0 0.0000
22 H 10.5390 12.0500 12.4720 H 0 UNK0 0.0000
23 H 11.2630 13.3950 13.3540 H 0 UNK0 0.0000
24 H 11.2610 13.3960 11.5910 H 0 UNK0 0.0000
25 H 13.5400 13.5640 13.7860 H 0 UNK0 0.0000
26 H 14.5190 12.1470 13.5030 H 0 UNK0 0.0000
27 N 15.5280 11.0210 10.9640 N.am 1 LEU1 0.0000
28 O 18.1440 8.6930 11.8020 O.co2 1 LEU1 -0.5000
29 CA 16.3760 9.8600 10.7000 C.3 1 LEU1 0.0000
30 OXT 17.5450 10.6850 12.5800 O.co2 1 LEU1 -0.5000
31 C 17.4530 9.7350 11.7760 C.2 1 LEU1 0.0000
32 CB 16.8770 9.9290 9.2380 C.3 1 LEU1 0.0000
33 CG 17.3260 8.5990 8.6000 C.3 1 LEU1 0.0000
34 CD2 16.2240 7.5230 8.6300 C.3 1 LEU1 0.0000
35 CD1 17.7800 8.8470 7.1540 C.3 1 LEU1 0.0000
36 H 15.9880 11.8670 11.2710 H 1 LEU1 0.0000
37 HA 15.7730 8.9640 10.8350 H 1 LEU1 0.0000
38 HG 18.1860 8.2260 9.1530 H 1 LEU1 0.0000
39 HB1 17.6850 10.6590 9.1710 H 1 LEU1 0.0000
40 HB2 16.0820 10.3340 8.6110 H 1 LEU1 0.0000
41 HD21 16.5150 6.6520 8.0460 H 1 LEU1 0.0000
42 HD22 16.0380 7.1630 9.6410 H 1 LEU1 0.0000
43 HD23 15.2850 7.8960 8.2210 H 1 LEU1 0.0000
44 HD11 18.1280 7.9340 6.6730 H 1 LEU1 0.0000
45 HD12 16.9680 9.2410 6.5490 H 1 LEU1 0.0000
46 HD13 18.5930 9.5670 7.1070 H 1 LEU1 0.0000
@<TRIPOS>BOND
1 1 3 1
2 1 15 1
3 1 2 1
4 1 7 1
5 27 5 am
6 27 29 1
7 27 36 1
8 28 31 ar
9 2 4 1
10 2 5 1
11 2 16 1
12 3 22 1
13 3 23 1
14 3 24 1
15 4 14 1
16 5 6 2
17 29 31 1
18 29 32 1
19 29 37 1
20 30 31 ar
21 7 25 1
22 7 26 1
23 7 8 1
24 8 13 ar
25 8 9 ar
26 9 10 ar
27 9 17 1
28 10 11 ar
29 10 18 1
30 11 12 ar
31 11 19 1
32 12 13 ar
33 12 20 1
34 13 21 1
35 32 39 1
36 32 33 1
37 32 40 1
38 33 38 1
39 33 34 1
40 33 35 1
41 34 41 1
42 34 43 1
43 34 42 1
44 35 45 1
45 35 44 1
46 35 46 1
@<TRIPOS>SUBSTRUCTURE
1 UNK0 1
2 LEU1 27
@<TRIPOS>COMMENT
0.0000
L


106 changes: 106 additions & 0 deletions data/ligands/lig_5y19.mol2
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@<TRIPOS>MOLECULE
pdb5y19.ent_out_ok
49 49 0 0 0
SMALL
GASTEIGER

@<TRIPOS>ATOM
1 N 11.5300 12.8000 12.8220 N.4 1 LIG 0.3822
2 C 12.7480 11.9890 12.6790 C.3 1 LIG -0.0443
3 C 13.4500 12.2270 11.3130 C.3 1 LIG 0.1186
4 O 12.4890 12.4620 10.3130 O.3 1 LIG -0.3842
5 C 13.7100 12.2270 13.8530 C.3 1 LIG -0.0379
6 C 13.2330 11.6380 15.1670 C.ar 1 LIG -0.0488
7 C 13.6500 10.3460 15.5510 C.ar 1 LIG -0.0586
8 C 12.4000 12.3850 16.0210 C.ar 1 LIG -0.0586
9 C 13.2640 9.8200 16.7980 C.ar 1 LIG -0.0615
10 C 11.9960 11.8470 17.2580 C.ar 1 LIG -0.0615
11 C 12.4350 10.5710 17.6530 C.ar 1 LIG -0.0617
12 N 15.5520 10.9890 10.9700 N.am 1 LIG -0.3019
13 O 13.5750 10.0200 10.4680 O.2 1 LIG -0.2730
14 N 18.3650 8.7020 11.6340 N.am 1 LIG -0.1960
15 O 17.5630 10.5550 12.6420 O.2 1 LIG -0.2717
16 O 19.0030 8.3370 12.8400 O.3 1 LIG -0.2951
17 C 14.2170 10.9780 10.8840 C.2 1 LIG 0.2406
18 C 16.4210 9.8520 10.6600 C.3 1 LIG 0.1016
19 C 16.8830 9.9270 9.1810 C.3 1 LIG -0.0236
20 C 17.4130 8.6180 8.5440 C.3 1 LIG -0.0446
21 C 17.8570 8.8540 7.0940 C.3 1 LIG -0.0626
22 C 16.3820 7.4780 8.5910 C.3 1 LIG -0.0626
23 C 17.5250 9.7430 11.7180 C.2 1 LIG 0.2558
24 H 16.0070 11.8350 11.2900 H 1 LIG 0.1495
25 H 18.2580 7.8940 11.0330 H 1 LIG 0.1823
26 H 12.3970 10.9580 12.7300 H 1 LIG 0.0117
27 H 13.8910 13.2960 13.9790 H 1 LIG 0.0298
28 H 14.6800 11.7840 13.6270 H 1 LIG 0.0298
29 H 14.2890 9.7640 14.9020 H 1 LIG 0.0620
30 H 12.0760 13.3740 15.7320 H 1 LIG 0.0620
31 H 13.5950 8.8360 17.0960 H 1 LIG 0.0618
32 H 11.3510 12.4110 17.9090 H 1 LIG 0.0618
33 H 12.1280 10.1640 18.6050 H 1 LIG 0.0618
34 H 12.9280 12.7860 9.5420 H 1 LIG 0.2103
35 H 18.4950 8.7930 13.4960 H 1 LIG 0.2414
36 H 14.1010 13.0980 11.3580 H 1 LIG 0.0673
37 H 10.6670 12.1510 12.8570 H 1 LIG -0.0895
38 H 11.5850 13.3750 13.7350 H 1 LIG -0.0895
39 H 11.4430 13.4700 11.9790 H 1 LIG -0.0895
40 H 15.8310 8.9510 10.7990 H 1 LIG 0.0595
41 H 18.3020 8.2930 9.0800 H 1 LIG 0.0296
42 H 17.6360 10.7110 9.0840 H 1 LIG 0.0290
43 H 16.0440 10.2670 8.5730 H 1 LIG 0.0290
44 H 18.2580 7.9440 6.6470 H 1 LIG 0.0232
45 H 17.0240 9.1890 6.4800 H 1 LIG 0.0232
46 H 18.6340 9.6090 7.0300 H 1 LIG 0.0232
47 H 16.7290 6.6130 8.0310 H 1 LIG 0.0232
48 H 16.2010 7.1310 9.6070 H 1 LIG 0.0232
49 H 15.4270 7.7850 8.1610 H 1 LIG 0.0232
@<TRIPOS>BOND
1 45 21 1
2 44 21 1
3 46 21 1
4 21 20 1
5 47 22 1
6 49 22 1
7 20 22 1
8 20 41 1
9 20 19 1
10 43 19 1
11 22 48 1
12 42 19 1
13 19 18 1
14 34 4 1
15 4 3 1
16 13 17 2
17 18 40 1
18 18 12 1
19 18 23 1
20 17 12 am
21 17 3 1
22 12 24 1
23 25 14 1
24 3 36 1
25 3 2 1
26 14 23 am
27 14 16 1
28 23 15 2
29 39 1 1
30 2 26 1
31 2 1 1
32 2 5 1
33 1 37 1
34 1 38 1
35 16 35 1
36 28 5 1
37 5 27 1
38 5 6 1
39 29 7 1
40 6 7 ar
41 6 8 ar
42 7 9 ar
43 30 8 1
44 8 10 ar
45 9 31 1
46 9 11 ar
47 10 11 ar
48 10 32 1
49 11 33 1
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