Mercurial > repos > bgruening > autodock_vina_prepare_receptor
comparison prepare_receptor.xml @ 1:8b9b960c9409 draft
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 |
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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> |