Mercurial > repos > bgruening > autodock_vina_prepare_ligand
comparison prepare_ligand.xml @ 2:f6eb53a200df draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author | bgruening |
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date | Tue, 07 May 2019 13:32:15 -0400 |
parents | 1b4a6ebd9898 |
children | 50871000e977 |
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1:1b4a6ebd9898 | 2:f6eb53a200df |
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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> |