Mercurial > repos > bgruening > autodock_vina_prepare_receptor

comparison prepare_receptor.xml @ 1:8b9b960c9409 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 13:32:31 -0400
parents d15e5a2a7558
children 05a13d377b28
comparison
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0:d15e5a2a7558 1:8b9b960c9409
1 <tool id="prepare_receptor" name="Prepare receptor" version="0.1.0"> 1 <tool id="prepare_receptor" name="Prepare receptor" version="0.1.0">
2 <description>Tool to prepare receptor for Autodock Vina</description> 2 <description>Tool to prepare receptor 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="receptor" value="3u1i_for_DM.pdb"/> 20 <param name="receptor" value="3u1i_for_DM.pdb"/>
21 <output name="file_output" file="3u1i_for_DM.pdbqt"/> 21 <output name="file_output" file="3u1i_for_DM.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 pdb molecule file to pdbqt molecule file, what is the Autodock Vina program uses to perform molecular docking. 26 .. class:: infomark
28 27
29 ** input ** 28 **What this tool does**
30 29
31 It's required at least one pdb dataset in history, what is informed in ligand field, for use the tool. The pdb molecule file looks like the following example: 30 This tool uses the MGLTools programming package to convert a pdb file to pdbqt file, which the Autodock Vina program uses to perform molecular docking. The output file has a similar format to the pdb input, with atom type modified to conform to AutoDock atom types and an extra column containing Gasteiger charges added.
32 31
32 -----
33
34 .. class:: infomark
35
36 **Input**
37
38 A pdb input file is required.
39
40 * Example::
41
33 ATOM 1 C ACE A 49 7.007 -4.529 9.096 1.00 0.00 C 42 ATOM 1 C ACE A 49 7.007 -4.529 9.096 1.00 0.00 C
34 ATOM 2 O ACE A 49 7.822 -3.710 8.650 1.00 0.00 O 43 ATOM 2 O ACE A 49 7.822 -3.710 8.650 1.00 0.00 O
35 ATOM 3 CH3 ACE A 49 6.132 -5.342 8.166 1.00 0.00 C 44 ATOM 3 CH3 ACE A 49 6.132 -5.342 8.166 1.00 0.00 C
36 ATOM 4 1HH3 ACE A 49 6.747 -5.942 7.510 1.00 0.00 H 45 ATOM 4 1HH3 ACE A 49 6.747 -5.942 7.510 1.00 0.00 H
37 ATOM 5 2HH3 ACE A 49 5.492 -5.996 8.739 1.00 0.00 H 46 ATOM 5 2HH3 ACE A 49 5.492 -5.996 8.739 1.00 0.00 H
56 ATOM 24 CA THR A 52 10.525 -4.607 17.507 1.00 55.35 C 65 ATOM 24 CA THR A 52 10.525 -4.607 17.507 1.00 55.35 C
57 ATOM 25 C THR A 52 11.729 -5.165 18.262 1.00 53.35 C 66 ATOM 25 C THR A 52 11.729 -5.165 18.262 1.00 53.35 C
58 ATOM 26 O THR A 52 12.413 -6.076 17.786 1.00 52.40 O 67 ATOM 26 O THR A 52 12.413 -6.076 17.786 1.00 52.40 O
59 ATOM 27 CB THR A 52 9.185 -4.964 18.195 1.00 56.95 C 68 ATOM 27 CB THR A 52 9.185 -4.964 18.195 1.00 56.95 C
60 69
61 ** output ** 70 -----
62 71
63 The output is a pdbqt molecule file converted from a pdb molecule file. The pdbqt molecule file looks like the following example: 72 .. class:: infomark
73
74 **Output**
75
76 The output is a pdbqt file - effectively the same as a pdb file, but with an extra column containing Gasteiger charges.
77
78 * Example::
64 79
65 ATOM 1 C ACE A 49 7.007 -4.529 9.096 1.00 0.00 0.214 C 80 ATOM 1 C ACE A 49 7.007 -4.529 9.096 1.00 0.00 0.214 C
66 ATOM 2 O ACE A 49 7.822 -3.710 8.650 1.00 0.00 -0.274 OA 81 ATOM 2 O ACE A 49 7.822 -3.710 8.650 1.00 0.00 -0.274 OA
67 ATOM 3 CH3 ACE A 49 6.132 -5.342 8.166 1.00 0.00 0.117 C 82 ATOM 3 CH3 ACE A 49 6.132 -5.342 8.166 1.00 0.00 0.117 C
68 ATOM 4 N ASP A 50 6.886 -4.713 10.549 1.00 65.94 -0.348 N 83 ATOM 4 N ASP A 50 6.886 -4.713 10.549 1.00 65.94 -0.348 N
83 ATOM 19 CG LEU A 51 12.250 -6.074 11.987 1.00 54.47 -0.020 C 98 ATOM 19 CG LEU A 51 12.250 -6.074 11.987 1.00 54.47 -0.020 C
84 ATOM 20 CD1 LEU A 51 13.717 -6.000 11.623 1.00 52.72 0.009 C 99 ATOM 20 CD1 LEU A 51 13.717 -6.000 11.623 1.00 52.72 0.009 C
85 ATOM 21 CD2 LEU A 51 11.857 -7.523 12.233 1.00 53.53 0.009 C 100 ATOM 21 CD2 LEU A 51 11.857 -7.523 12.233 1.00 53.53 0.009 C
86 ATOM 22 N THR A 52 10.527 -5.061 16.117 1.00 55.68 -0.344 N 101 ATOM 22 N THR A 52 10.527 -5.061 16.117 1.00 55.68 -0.344 N
87 ATOM 23 HN THR A 52 10.475 -6.064 15.941 1.00 0.00 0.163 HD 102 ATOM 23 HN THR A 52 10.475 -6.064 15.941 1.00 0.00 0.163 HD
88 ]]></help> 103
104
105 ]]></help>
89 <citations> 106 <citations>
90 <citation type="doi">10.1002/jcc.21334</citation> 107 <citation type="doi">10.1002/jcc.21334</citation>
91 </citations> 108 </citations>
92 </tool> 109 </tool>