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comparison prepare_ligand.xml @ 2:f6eb53a200df draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:32:15 -0400
parents 1b4a6ebd9898
children 50871000e977
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1:1b4a6ebd9898 2:f6eb53a200df
1 <tool id="prepare_ligand" name="Prepare ligand" version="0.1.0"> 1 <tool id="prepare_ligand" name="Prepare ligand" version="0.1.0">
2 <description>Tool to prepare ligand for Autodock Vina</description> 2 <description>for docking with Autodock Vina</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.5.6">mgltools</requirement> 4 <requirement type="package" version="1.5.6">mgltools</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1" /> 7 <exit_code range="1" />
20 <param name="ligand" value="NuBBE_1_obabel_3D.mol2"/> 20 <param name="ligand" value="NuBBE_1_obabel_3D.mol2"/>
21 <output name="file_output" file="NuBBE_1_obabel_3D.pdbqt"/> 21 <output name="file_output" file="NuBBE_1_obabel_3D.pdbqt"/>
22 </test> 22 </test>
23 </tests> 23 </tests>
24 <help><![CDATA[ 24 <help><![CDATA[
25 **What it does?**
26 25
27 This tool uses the MGLTools programming packages to convert a mol2 molecule file to pdbqt molecule file, what is the Autodock Vina program uses to perform molecular docking. 26 .. class:: infomark
27
28 **What this tool does**
29
30 This tool uses the MGLTools programming package to convert a mol2 molecule file to a pdbqt molecule file, which the Autodock Vina program uses to perform molecular docking. The output file has a similar format to the pdb input, with atom types modified to conform to AutoDock atom types and an extra column containing Gasteiger charges added.
31
32 -----
33
34 .. class:: infomark
28 35
29 **Input** 36 **Input**
30 37
31 It's required at least one mol2 dataset in history, what is informed in ligand field, for use the tool. The mol2 molecule file looks like the following example:: 38 A mol2 file is required to use this tool.
32 39
33 @<TRIPOS>MOLECULE 40 * Example::
34 NuBBE_1
35 21 21 0 0 0
36 SMALL
37 GASTEIGER
38 41
39 @<TRIPOS>ATOM 42 @<TRIPOS>MOLECULE
40 1 O -0.9469 -0.4359 -3.2099 O.2 1 LIG1 -0.2449 43 NuBBE_1
41 2 C -1.2069 0.2449 -2.2351 C.2 1 LIG1 0.3396 44 21 21 0 0 0
42 3 O -1.9353 -0.1138 -1.1515 O.3 1 LIG1 -0.4570 45 SMALL
43 4 C -2.3385 -1.4828 -1.0650 C.3 1 LIG1 0.1113 46 GASTEIGER
44 5 C -1.7447 -2.0319 0.2001 C.2 1 LIG1 -0.0480 47 @<TRIPOS>ATOM
45 6 C -0.5501 -2.6439 0.3381 C.2 1 LIG1 -0.0731 48 1 O -0.9469 -0.4359 -3.2099 O.2 1 LIG1 -0.2449
46 7 C 0.4046 -2.8855 -0.8015 C.3 1 LIG1 -0.0437 49 2 C -1.2069 0.2449 -2.2351 C.2 1 LIG1 0.3396
47 8 C -0.0862 -3.1529 1.6937 C.3 1 LIG1 -0.0285 50 3 O -1.9353 -0.1138 -1.1515 O.3 1 LIG1 -0.4570
48 9 C 0.7304 -2.1137 2.4728 C.3 1 LIG1 -0.0308 51 4 C -2.3385 -1.4828 -1.0650 C.3 1 LIG1 0.1113
49 10 C 1.1870 -2.6184 3.8183 C.2 1 LIG1 -0.0850 52 5 C -1.7447 -2.0319 0.2001 C.2 1 LIG1 -0.0480
50 11 C 2.3521 -3.2333 4.1099 C.2 1 LIG1 -0.0796 53 6 C -0.5501 -2.6439 0.3381 C.2 1 LIG1 -0.0731
51 12 C 3.4007 -3.6048 3.0986 C.3 1 LIG1 -0.0440 54 7 C 0.4046 -2.8855 -0.8015 C.3 1 LIG1 -0.0437
52 13 C 2.6989 -3.6136 5.5272 C.3 1 LIG1 -0.0440 55 8 C -0.0862 -3.1529 1.6937 C.3 1 LIG1 -0.0285
53 14 C -0.7776 1.6572 -2.0661 C.ar 1 LIG1 0.0627 56 9 C 0.7304 -2.1137 2.4728 C.3 1 LIG1 -0.0308
54 15 C -0.6402 2.2240 -0.7903 C.ar 1 LIG1 -0.0026 57 10 C 1.1870 -2.6184 3.8183 C.2 1 LIG1 -0.0850
55 16 C -0.2486 3.5509 -0.6768 C.ar 1 LIG1 0.1590 58 11 C 2.3521 -3.2333 4.1099 C.2 1 LIG1 -0.0796
56 17 O -0.1045 4.1587 0.5397 O.3 1 LIG1 -0.5033 59 12 C 3.4007 -3.6048 3.0986 C.3 1 LIG1 -0.0440
57 18 C 0.0124 4.3080 -1.8161 C.ar 1 LIG1 0.1583 60 13 C 2.6989 -3.6136 5.5272 C.3 1 LIG1 -0.0440
58 19 O 0.3891 5.6141 -1.6913 O.3 1 LIG1 -0.5033 61 14 C -0.7776 1.6572 -2.0661 C.ar 1 LIG1 0.0627
59 20 C -0.1020 3.7535 -3.0825 C.ar 1 LIG1 -0.0158 62 15 C -0.6402 2.2240 -0.7903 C.ar 1 LIG1 -0.0026
60 21 C -0.4936 2.4191 -3.2122 C.ar 1 LIG1 -0.0441 63 16 C -0.2486 3.5509 -0.6768 C.ar 1 LIG1 0.1590
61 @<TRIPOS>BOND 64 17 O -0.1045 4.1587 0.5397 O.3 1 LIG1 -0.5033
62 1 1 2 2 65 18 C 0.0124 4.3080 -1.8161 C.ar 1 LIG1 0.1583
63 2 2 3 1 66 19 O 0.3891 5.6141 -1.6913 O.3 1 LIG1 -0.5033
64 3 3 4 1 67 20 C -0.1020 3.7535 -3.0825 C.ar 1 LIG1 -0.0158
65 4 4 5 1 68 21 C -0.4936 2.4191 -3.2122 C.ar 1 LIG1 -0.0441
66 5 5 6 2 69 @<TRIPOS>BOND
67 6 6 7 1 70 1 1 2 2
68 7 6 8 1 71 2 2 3 1
69 8 8 9 1 72 3 3 4 1
70 9 9 10 1 73 4 4 5 1
71 10 10 11 2 74 5 5 6 2
72 11 11 12 1 75 6 6 7 1
73 12 11 13 1 76 7 6 8 1
74 13 2 14 1 77 8 8 9 1
75 14 14 15 ar 78 9 9 10 1
76 15 15 16 ar 79 10 10 11 2
77 16 16 17 1 80 11 11 12 1
78 17 16 18 ar 81 12 11 13 1
79 18 18 19 1 82 13 2 14 1
80 19 18 20 ar 83 14 14 15 ar
81 20 20 21 ar 84 15 15 16 ar
82 21 14 21 ar 85 16 16 17 1
86 17 16 18 ar
87 18 18 19 1
88 19 18 20 ar
89 20 20 21 ar
90 21 14 21 ar
91
92 -----
93
94 .. class:: infomark
83 95
84 **Output** 96 **Output**
85 97
86 The output is a pdbqt molecule file converted from a mol2 molecule file. The pdbqt molecule file looks like the following example:: 98 The output is a pdbqt molecule file.
87 99
88 REMARK 9 active torsions: 100 * Example::
89 REMARK status: ('A' for Active; 'I' for Inactive)
90 REMARK 1 A between atoms: C_2 and O_3
91 REMARK 2 A between atoms: C_2 and C_14
92 REMARK 3 A between atoms: O_3 and C_4
93 REMARK 4 A between atoms: C_4 and C_5
94 REMARK 5 A between atoms: C_6 and C_8
95 REMARK 6 A between atoms: C_8 and C_9
96 REMARK 7 A between atoms: C_9 and C_10
97 REMARK 8 A between atoms: C_16 and O_17
98 REMARK 9 A between atoms: C_19 and O_20
99 ROOT
100 ATOM 1 O LIG d 1 -0.947 -0.436 -3.210 0.00 0.00 -0.259 OA
101 ATOM 2 C LIG d 1 -1.207 0.245 -2.235 0.00 0.00 0.293 C
102 ENDROOT
103 BRANCH 2 3
104 ATOM 3 O LIG d 1 -1.935 -0.114 -1.151 0.00 0.00 -0.314 OA
105 BRANCH 3 4
106 ATOM 4 C LIG d 1 -2.338 -1.483 -1.065 0.00 0.00 0.206 C
107 BRANCH 4 5
108 ATOM 5 C LIG d 1 -1.745 -2.032 0.200 0.00 0.00 0.002 C
109 ATOM 6 C LIG d 1 -0.550 -2.644 0.338 0.00 0.00 -0.085 C
110 ATOM 7 C LIG d 1 0.405 -2.885 -0.801 0.00 0.00 0.043 C
111 BRANCH 6 8
112 ATOM 8 C LIG d 1 -0.086 -3.153 1.694 0.00 0.00 0.037 C
113 BRANCH 8 9
114 ATOM 9 C LIG d 1 0.730 -2.114 2.473 0.00 0.00 0.031 C
115 BRANCH 9 10
116 ATOM 10 C LIG d 1 1.187 -2.618 3.818 0.00 0.00 -0.024 C
117 ATOM 11 C LIG d 1 2.352 -3.233 4.110 0.00 0.00 -0.091 C
118 ATOM 12 C LIG d 1 3.401 -3.605 3.099 0.00 0.00 0.042 C
119 ATOM 13 C LIG d 1 2.699 -3.614 5.527 0.00 0.00 0.042 C
120 ENDBRANCH 9 10
121 ENDBRANCH 8 9
122 ENDBRANCH 6 8
123 ENDBRANCH 4 5
124 ENDBRANCH 3 4
125 ENDBRANCH 2 3
126 BRANCH 2 14
127 ATOM 14 C LIG d 1 -0.778 1.657 -2.066 0.00 0.00 0.042 A
128 ATOM 15 C LIG d 1 -0.640 2.224 -0.790 0.00 0.00 0.057 A
129 ATOM 16 C LIG d 1 -0.249 3.551 -0.677 0.00 0.00 0.099 A
130 ATOM 17 C LIG d 1 0.012 4.308 -1.816 0.00 0.00 0.098 A
131 ATOM 18 C LIG d 1 -0.102 3.753 -3.083 0.00 0.00 0.040 A
132 ATOM 19 C LIG d 1 -0.494 2.419 -3.212 0.00 0.00 0.020 A
133 BRANCH 16 20
134 ATOM 20 O LIG d 1 -0.104 4.159 0.540 0.00 0.00 -0.358 OA
135 ATOM 21 HO LIG d 1 0.164 5.067 0.617 1.00 0.00 0.217 HD
136 ENDBRANCH 16 20
137 BRANCH 17 22
138 ATOM 22 O LIG d 1 0.389 5.614 -1.691 0.00 0.00 -0.358 OA
139 ATOM 23 HO LIG d 1 0.567 6.131 -2.469 1.00 0.00 0.217 HD
140 ENDBRANCH 17 22
141 ENDBRANCH 2 14
142 TORSDOF 9
143 101
102 REMARK 9 active torsions:
103 REMARK status: ('A' for Active; 'I' for Inactive)
104 REMARK 1 A between atoms: C_2 and O_3
105 REMARK 2 A between atoms: C_2 and C_14
106 REMARK 3 A between atoms: O_3 and C_4
107 REMARK 4 A between atoms: C_4 and C_5
108 REMARK 5 A between atoms: C_6 and C_8
109 REMARK 6 A between atoms: C_8 and C_9
110 REMARK 7 A between atoms: C_9 and C_10
111 REMARK 8 A between atoms: C_16 and O_17
112 REMARK 9 A between atoms: C_19 and O_20
113 ROOT
114 ATOM 1 O LIG d 1 -0.947 -0.436 -3.210 0.00 0.00 -0.259 OA
115 ATOM 2 C LIG d 1 -1.207 0.245 -2.235 0.00 0.00 0.293 C
116 ENDROOT
117 BRANCH 2 3
118 ATOM 3 O LIG d 1 -1.935 -0.114 -1.151 0.00 0.00 -0.314 OA
119 BRANCH 3 4
120 ATOM 4 C LIG d 1 -2.338 -1.483 -1.065 0.00 0.00 0.206 C
121 BRANCH 4 5
122 ATOM 5 C LIG d 1 -1.745 -2.032 0.200 0.00 0.00 0.002 C
123 ATOM 6 C LIG d 1 -0.550 -2.644 0.338 0.00 0.00 -0.085 C
124 ATOM 7 C LIG d 1 0.405 -2.885 -0.801 0.00 0.00 0.043 C
125 BRANCH 6 8
126 ATOM 8 C LIG d 1 -0.086 -3.153 1.694 0.00 0.00 0.037 C
127 BRANCH 8 9
128 ATOM 9 C LIG d 1 0.730 -2.114 2.473 0.00 0.00 0.031 C
129 BRANCH 9 10
130 ATOM 10 C LIG d 1 1.187 -2.618 3.818 0.00 0.00 -0.024 C
131 ATOM 11 C LIG d 1 2.352 -3.233 4.110 0.00 0.00 -0.091 C
132 ATOM 12 C LIG d 1 3.401 -3.605 3.099 0.00 0.00 0.042 C
133 ATOM 13 C LIG d 1 2.699 -3.614 5.527 0.00 0.00 0.042 C
134 ENDBRANCH 9 10
135 ENDBRANCH 8 9
136 ENDBRANCH 6 8
137 ENDBRANCH 4 5
138 ENDBRANCH 3 4
139 ENDBRANCH 2 3
140 BRANCH 2 14
141 ATOM 14 C LIG d 1 -0.778 1.657 -2.066 0.00 0.00 0.042 A
142 ATOM 15 C LIG d 1 -0.640 2.224 -0.790 0.00 0.00 0.057 A
143 ATOM 16 C LIG d 1 -0.249 3.551 -0.677 0.00 0.00 0.099 A
144 ATOM 17 C LIG d 1 0.012 4.308 -1.816 0.00 0.00 0.098 A
145 ATOM 18 C LIG d 1 -0.102 3.753 -3.083 0.00 0.00 0.040 A
146 ATOM 19 C LIG d 1 -0.494 2.419 -3.212 0.00 0.00 0.020 A
147 BRANCH 16 20
148 ATOM 20 O LIG d 1 -0.104 4.159 0.540 0.00 0.00 -0.358 OA
149 ATOM 21 HO LIG d 1 0.164 5.067 0.617 1.00 0.00 0.217 HD
150 ENDBRANCH 16 20
151 BRANCH 17 22
152 ATOM 22 O LIG d 1 0.389 5.614 -1.691 0.00 0.00 -0.358 OA
153 ATOM 23 HO LIG d 1 0.567 6.131 -2.469 1.00 0.00 0.217 HD
154 ENDBRANCH 17 22
155 ENDBRANCH 2 14
156 TORSDOF 9
144 ]]></help> 157 ]]></help>
145 <citations> 158 <citations>
146 <citation type="doi">10.1002/jcc.21334</citation> 159 <citation type="doi">10.1002/jcc.21334</citation>
147 </citations> 160 </citations>
148 </tool> 161 </tool>