Mercurial > repos > bgruening > autodock_vina

comparison docking.xml @ 4:3c8e86318a81 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
author bgruening
date Mon, 12 Feb 2018 04:23:13 -0500
parents 65ffed035ca8
children c410ffcabf9d
comparison
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3:65ffed035ca8 4:3c8e86318a81
26 <output name="file_output1" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt"/> 26 <output name="file_output1" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt"/>
27 <output name="file_output2" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.log"/> 27 <output name="file_output2" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.log"/>
28 </test> 28 </test>
29 </tests> 29 </tests>
30 <help><![CDATA[ 30 <help><![CDATA[
31 ** What it does? ** 31 **What it does?**
32 32
33 This tool performs molecular docking with Autodock Vina program. 33 This tool performs molecular docking with Autodock Vina program.
34 34
35 ** inputs ** 35 **Inputs**
36 36
37 Three inputs are required for use this tools. The first is a text file with the box configurations, this file looks like the following example: 37 Three inputs are required for use this tools. The first is a text file with the box configurations, this file looks like the following example::
38 38
39 size_x = 20.00 39 size_x = 20.00
40 size_y = 18.40 40 size_y = 18.40
41 size_z = 23.60 41 size_z = 23.60
42 center_x = 70.92 42 center_x = 70.92
43 center_y = 70.57 43 center_y = 70.57
44 center_z = 36.86 44 center_z = 36.86
45 num_modes = 9999 45 num_modes = 9999
46 energy_range = 9999 46 energy_range = 9999
47 exhaustiveness = 10 47 exhaustiveness = 10
48 cpu = 4 48 cpu = 4
49 seed = 1 49 seed = 1
50 50
51 Where the parameters size_x, size_y, size_z, center_x, center_y and center_z are coordinates of the binding site. 51 Where the parameters size_x, size_y, size_z, center_x, center_y and center_z are coordinates of the binding site.
52 The parameters num_modes, energy_range, exhaustiveness, cpu and seed are autodock vina configurations to execute the algorithm. 52 The parameters num_modes, energy_range, exhaustiveness, cpu and seed are autodock vina configurations to execute the algorithm.
53 53
54 The second input is a receptor file (pdbqt) what is a output of the prepare receptor tool. 54 The second input is a receptor file (pdbqt) what is a output of the prepare receptor tool.
55 The last input is a ligand file (pdbqt) what is a output of the prepare ligand tool. 55 The last input is a ligand file (pdbqt) what is a output of the prepare ligand tool.
56 56
57 ** outputs ** 57 **Outputs**
58 58
59 Two outputs are generated by this tool. The first is a pdbqt file with the molecule structure resulting of the molecular docking, this file looks like the following example: 59 Two outputs are generated by this tool. The first is a pdbqt file with the molecule structure resulting of the molecular docking, this file looks like the following example::
60 60
61 MODEL 1 61 MODEL 1
62 REMARK VINA RESULT: -0.0 0.000 0.000 62 REMARK VINA RESULT: -0.0 0.000 0.000
63 REMARK 9 active torsions: 63 REMARK 9 active torsions:
64 REMARK status: ('A' for Active; 'I' for Inactive) 64 REMARK status: ('A' for Active; 'I' for Inactive)
65 REMARK 1 A between atoms: C_2 and O_3 65 REMARK 1 A between atoms: C_2 and O_3
66 REMARK 2 A between atoms: C_2 and C_14 66 REMARK 2 A between atoms: C_2 and C_14
67 REMARK 3 A between atoms: O_3 and C_4 67 REMARK 3 A between atoms: O_3 and C_4
68 REMARK 4 A between atoms: C_4 and C_5 68 REMARK 4 A between atoms: C_4 and C_5
69 REMARK 5 A between atoms: C_6 and C_8 69 REMARK 5 A between atoms: C_6 and C_8
70 REMARK 6 A between atoms: C_8 and C_9 70 REMARK 6 A between atoms: C_8 and C_9
71 REMARK 7 A between atoms: C_9 and C_10 71 REMARK 7 A between atoms: C_9 and C_10
72 REMARK 8 A between atoms: C_16 and O_17 72 REMARK 8 A between atoms: C_16 and O_17
73 REMARK 9 A between atoms: C_19 and O_20 73 REMARK 9 A between atoms: C_19 and O_20
74 ROOT 74 ROOT
75 ATOM 1 O LIG d 1 72.801 71.157 37.352 0.00 0.00 -0.259 OA 75 ATOM 1 O LIG d 1 72.801 71.157 37.352 0.00 0.00 -0.259 OA
76 ATOM 2 C LIG d 1 73.413 72.112 37.794 0.00 0.00 0.293 C 76 ATOM 2 C LIG d 1 73.413 72.112 37.794 0.00 0.00 0.293 C
77 ENDROOT 77 ENDROOT
78 BRANCH 2 3 78 BRANCH 2 3
79 ATOM 3 O LIG d 1 72.912 73.321 38.144 0.00 0.00 -0.314 OA 79 ATOM 3 O LIG d 1 72.912 73.321 38.144 0.00 0.00 -0.314 OA
80 BRANCH 3 4 80 BRANCH 3 4
81 ATOM 4 C LIG d 1 71.868 73.332 39.120 0.00 0.00 0.206 C 81 ATOM 4 C LIG d 1 71.868 73.332 39.120 0.00 0.00 0.206 C
82 BRANCH 4 5 82 BRANCH 4 5
83 ATOM 5 C LIG d 1 72.522 73.555 40.453 0.00 0.00 0.002 C 83 ATOM 5 C LIG d 1 72.522 73.555 40.453 0.00 0.00 0.002 C
84 ATOM 6 C LIG d 1 72.762 72.629 41.405 0.00 0.00 -0.085 C 84 ATOM 6 C LIG d 1 72.762 72.629 41.405 0.00 0.00 -0.085 C
85 ATOM 7 C LIG d 1 72.390 71.176 41.274 0.00 0.00 0.043 C 85 ATOM 7 C LIG d 1 72.390 71.176 41.274 0.00 0.00 0.043 C
86 BRANCH 6 8 86 BRANCH 6 8
87 ATOM 8 C LIG d 1 73.435 73.012 42.714 0.00 0.00 0.037 C 87 ATOM 8 C LIG d 1 73.435 73.012 42.714 0.00 0.00 0.037 C
88 BRANCH 8 9 88 BRANCH 8 9
89 ATOM 9 C LIG d 1 74.184 74.348 42.631 0.00 0.00 0.031 C 89 ATOM 9 C LIG d 1 74.184 74.348 42.631 0.00 0.00 0.031 C
90 BRANCH 9 10 90 BRANCH 9 10
91 ATOM 10 C LIG d 1 75.668 74.175 42.431 0.00 0.00 -0.024 C 91 ATOM 10 C LIG d 1 75.668 74.175 42.431 0.00 0.00 -0.024 C
92 ATOM 11 C LIG d 1 76.399 74.547 41.360 0.00 0.00 -0.091 C 92 ATOM 11 C LIG d 1 76.399 74.547 41.360 0.00 0.00 -0.091 C
93 ATOM 12 C LIG d 1 75.833 75.151 40.104 0.00 0.00 0.042 C 93 ATOM 12 C LIG d 1 75.833 75.151 40.104 0.00 0.00 0.042 C
94 ATOM 13 C LIG d 1 77.897 74.373 41.339 0.00 0.00 0.042 C 94 ATOM 13 C LIG d 1 77.897 74.373 41.339 0.00 0.00 0.042 C
95 ENDBRANCH 9 10 95 ENDBRANCH 9 10
96 ENDBRANCH 8 9 96 ENDBRANCH 8 9
97 ENDBRANCH 6 8 97 ENDBRANCH 6 8
98 ENDBRANCH 4 5 98 ENDBRANCH 4 5
99 ENDBRANCH 3 4 99 ENDBRANCH 3 4
100 ENDBRANCH 2 3 100 ENDBRANCH 2 3
101 BRANCH 2 14 101 BRANCH 2 14
102 ATOM 14 C LIG d 1 74.882 72.132 38.012 0.00 0.00 0.042 A 102 ATOM 14 C LIG d 1 74.882 72.132 38.012 0.00 0.00 0.042 A
103 ATOM 15 C LIG d 1 75.732 72.845 37.153 0.00 0.00 0.057 A 103 ATOM 15 C LIG d 1 75.732 72.845 37.153 0.00 0.00 0.057 A
104 ATOM 16 C LIG d 1 77.101 72.826 37.385 0.00 0.00 0.099 A 104 ATOM 16 C LIG d 1 77.101 72.826 37.385 0.00 0.00 0.099 A
105 ATOM 17 C LIG d 1 77.623 72.116 38.462 0.00 0.00 0.098 A 105 ATOM 17 C LIG d 1 77.623 72.116 38.462 0.00 0.00 0.098 A
106 ATOM 18 C LIG d 1 76.791 71.422 39.330 0.00 0.00 0.040 A 106 ATOM 18 C LIG d 1 76.791 71.422 39.330 0.00 0.00 0.040 A
107 ATOM 19 C LIG d 1 75.412 71.432 39.110 0.00 0.00 0.020 A 107 ATOM 19 C LIG d 1 75.412 71.432 39.110 0.00 0.00 0.020 A
108 BRANCH 16 20 108 BRANCH 16 20
109 ATOM 20 O LIG d 1 77.978 73.498 36.578 0.00 0.00 -0.358 OA 109 ATOM 20 O LIG d 1 77.978 73.498 36.578 0.00 0.00 -0.358 OA
110 ATOM 21 HO LIG d 1 77.680 74.093 35.900 1.00 0.00 0.217 HD 110 ATOM 21 HO LIG d 1 77.680 74.093 35.900 1.00 0.00 0.217 HD
111 ENDBRANCH 16 20 111 ENDBRANCH 16 20
112 BRANCH 17 22 112 BRANCH 17 22
113 ATOM 22 O LIG d 1 78.971 72.100 38.675 0.00 0.00 -0.358 OA 113 ATOM 22 O LIG d 1 78.971 72.100 38.675 0.00 0.00 -0.358 OA
114 ATOM 23 HO LIG d 1 79.541 71.651 38.060 1.00 0.00 0.217 HD 114 ATOM 23 HO LIG d 1 79.541 71.651 38.060 1.00 0.00 0.217 HD
115 ENDBRANCH 17 22 115 ENDBRANCH 17 22
116 ENDBRANCH 2 14 116 ENDBRANCH 2 14
117 TORSDOF 9 117 TORSDOF 9
118 ENDMDL 118 ENDMDL
119 119
120 The last is a log file with the binding affinity scores, this file looks like the following example: 120 The last is a log file with the binding affinity scores, this file looks like the following example::
121 121
122 ----------------------------------------------------------------- 122 -----------------------------------------------------------------
123 If you used AutoDock Vina in your work, please cite: 123 If you used AutoDock Vina in your work, please cite:
124 124
125 O. Trott, A. J. Olson, 125 O. Trott, A. J. Olson,
126 AutoDock Vina: improving the speed and accuracy of docking 126 AutoDock Vina: improving the speed and accuracy of docking
127 with a new scoring function, efficient optimization and 127 with a new scoring function, efficient optimization and
128 multithreading, Journal of Computational Chemistry 31 (2010) 128 multithreading, Journal of Computational Chemistry 31 (2010)
129 455-461 129 455-461
130 130
131 DOI 10.1002/jcc.21334 131 DOI 10.1002/jcc.21334
132 132
133 Please see http://vina.scripps.edu for more information. 133 Please see http://vina.scripps.edu for more information.
134 ------------------------------------------------------------------ 134 ------------------------------------------------------------------
135 135
136 Reading input ... done. 136 Reading input ... done.
137 Setting up the scoring function ... done. 137 Setting up the scoring function ... done.
138 Analyzing the binding site ... done. 138 Analyzing the binding site ... done.
139 Using random seed: 1899908181 139 Using random seed: 1899908181
140 Performing search ... done. 140 Performing search ... done.
141 Refining results ... done. 141 Refining results ... done.
142 142
143 mode | affinity | dist from best mode 143 mode | affinity | dist from best mode
144 | (kcal/mol) | rmsd l.b.| rmsd u.b. 144 | (kcal/mol) | rmsd l.b.| rmsd u.b.
145 -----+------------+----------+---------- 145 -----+------------+----------+----------
146 1 -0.0 0.000 0.000 146 1 -0.0 0.000 0.000
147 2 -0.0 2.046 2.443 147 2 -0.0 2.046 2.443
148 3 -0.0 5.896 7.949 148 3 -0.0 5.896 7.949
149 4 -0.0 2.518 3.100 149 4 -0.0 2.518 3.100
150 5 -0.0 2.417 4.527 150 5 -0.0 2.417 4.527
151 6 -0.0 5.686 7.689 151 6 -0.0 5.686 7.689
152 7 -0.0 2.828 4.792 152 7 -0.0 2.828 4.792
153 8 -0.0 5.547 7.086 153 8 -0.0 5.547 7.086
154 9 -0.0 7.388 9.966 154 9 -0.0 7.388 9.966
155 10 -0.0 7.877 11.352 155 10 -0.0 7.877 11.352
156 11 -0.0 8.203 10.157 156 11 -0.0 8.203 10.157
157 12 -0.0 5.163 7.653 157 12 -0.0 5.163 7.653
158 13 -0.0 3.093 6.011 158 13 -0.0 3.093 6.011
159 14 -0.0 7.998 11.146 159 14 -0.0 7.998 11.146
160 15 -0.0 7.015 10.108 160 15 -0.0 7.015 10.108
161 16 -0.0 8.795 11.682 161 16 -0.0 8.795 11.682
162 17 -0.0 7.317 10.367 162 17 -0.0 7.317 10.367
163 18 0.0 3.274 4.160 163 18 0.0 3.274 4.160
164 19 0.0 10.286 12.001 164 19 0.0 10.286 12.001
165 20 0.0 3.566 5.349 165 20 0.0 3.566 5.349
166 Writing output ... done. 166 Writing output ... done.
167 ]]></help> 167 ]]></help>
168 <citations> 168 <citations>
169 <citation type="doi">10.1002/jcc.21334</citation> 169 <citation type="doi">10.1002/jcc.21334</citation>
170 </citations> 170 </citations>
171 </tool> 171 </tool>