Mercurial > repos > bgruening > autodock_vina_prepare_receptor
view 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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<tool id="prepare_receptor" name="Prepare receptor" version="0.1.0"> <description>Tool to prepare receptor for docking with Autodock Vina</description> <requirements> <requirement type="package" version="1.5.6">mgltools</requirement> </requirements> <stdio> <exit_code range="1" /> </stdio> <command><![CDATA[ ln -s $receptor ./receptor.pdb && prepare_receptor4.py -r ./receptor.pdb -o "$file_output" -v -U nphs_lps -A hydrogens ]]></command> <inputs> <param type="data" name="receptor" format="pdb" label="Select a PDB file" /> </inputs> <outputs> <data name="file_output" format="pdbqt" /> </outputs> <tests> <test> <param name="receptor" value="3u1i_for_DM.pdb"/> <output name="file_output" file="3u1i_for_DM.pdbqt"/> </test> </tests> <help><![CDATA[ .. class:: infomark **What this tool does** 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. ----- .. class:: infomark **Input** A pdb input file is required. * Example:: ATOM 1 C ACE A 49 7.007 -4.529 9.096 1.00 0.00 C ATOM 2 O ACE A 49 7.822 -3.710 8.650 1.00 0.00 O ATOM 3 CH3 ACE A 49 6.132 -5.342 8.166 1.00 0.00 C ATOM 4 1HH3 ACE A 49 6.747 -5.942 7.510 1.00 0.00 H ATOM 5 2HH3 ACE A 49 5.492 -5.996 8.739 1.00 0.00 H ATOM 6 3HH3 ACE A 49 5.518 -4.686 7.568 1.00 0.00 H ATOM 7 N ASP A 50 6.886 -4.713 10.549 1.00 65.94 N ATOM 8 CA ASP A 50 7.845 -3.806 11.248 1.00 64.98 C ATOM 9 C ASP A 50 8.508 -4.537 12.430 1.00 62.63 C ATOM 10 O ASP A 50 7.898 -5.423 13.032 1.00 63.05 O ATOM 11 CB ASP A 50 7.146 -2.511 11.685 1.00 66.87 C ATOM 12 CG ASP A 50 8.017 -1.267 11.465 1.00 68.22 C ATOM 13 OD1 ASP A 50 9.140 -1.204 12.030 1.00 67.77 O ATOM 14 OD2 ASP A 50 7.570 -0.351 10.729 1.00 69.97 O1- ATOM 15 N LEU A 51 9.760 -4.189 12.730 1.00 60.07 N ATOM 16 CA LEU A 51 10.551 -4.934 13.712 1.00 57.24 C ATOM 17 C LEU A 51 10.592 -4.245 15.069 1.00 56.84 C ATOM 18 O LEU A 51 10.689 -3.020 15.157 1.00 57.09 O ATOM 19 CB LEU A 51 11.979 -5.179 13.205 1.00 55.78 C ATOM 20 CG LEU A 51 12.250 -6.074 11.987 1.00 54.47 C ATOM 21 CD1 LEU A 51 13.717 -6.000 11.623 1.00 52.72 C ATOM 22 CD2 LEU A 51 11.857 -7.523 12.233 1.00 53.53 C ATOM 23 N THR A 52 10.527 -5.061 16.117 1.00 55.68 N ATOM 24 CA THR A 52 10.525 -4.607 17.507 1.00 55.35 C ATOM 25 C THR A 52 11.729 -5.165 18.262 1.00 53.35 C ATOM 26 O THR A 52 12.413 -6.076 17.786 1.00 52.40 O ATOM 27 CB THR A 52 9.185 -4.964 18.195 1.00 56.95 C ----- .. class:: infomark **Output** The output is a pdbqt file - effectively the same as a pdb file, but with an extra column containing Gasteiger charges. * Example:: ATOM 1 C ACE A 49 7.007 -4.529 9.096 1.00 0.00 0.214 C ATOM 2 O ACE A 49 7.822 -3.710 8.650 1.00 0.00 -0.274 OA ATOM 3 CH3 ACE A 49 6.132 -5.342 8.166 1.00 0.00 0.117 C ATOM 4 N ASP A 50 6.886 -4.713 10.549 1.00 65.94 -0.348 N ATOM 5 HN ASP A 50 6.246 -5.360 11.009 1.00 0.00 0.163 HD ATOM 6 CA ASP A 50 7.845 -3.806 11.248 1.00 64.98 0.186 C ATOM 7 C ASP A 50 8.508 -4.537 12.430 1.00 62.63 0.241 C ATOM 8 O ASP A 50 7.898 -5.423 13.032 1.00 63.05 -0.271 OA ATOM 9 CB ASP A 50 7.146 -2.511 11.685 1.00 66.87 0.147 C ATOM 10 CG ASP A 50 8.017 -1.267 11.465 1.00 68.22 0.175 C ATOM 11 OD1 ASP A 50 9.140 -1.204 12.030 1.00 67.77 -0.648 OA ATOM 12 OD2 ASP A 50 7.570 -0.351 10.729 1.00 69.97 -0.648 OA ATOM 13 N LEU A 51 9.760 -4.189 12.730 1.00 60.07 -0.346 N ATOM 14 HN LEU A 51 10.177 -3.384 12.264 1.00 0.00 0.163 HD ATOM 15 CA LEU A 51 10.551 -4.934 13.712 1.00 57.24 0.177 C ATOM 16 C LEU A 51 10.592 -4.245 15.069 1.00 56.84 0.241 C ATOM 17 O LEU A 51 10.689 -3.020 15.157 1.00 57.09 -0.271 OA ATOM 18 CB LEU A 51 11.979 -5.179 13.205 1.00 55.78 0.038 C ATOM 19 CG LEU A 51 12.250 -6.074 11.987 1.00 54.47 -0.020 C ATOM 20 CD1 LEU A 51 13.717 -6.000 11.623 1.00 52.72 0.009 C ATOM 21 CD2 LEU A 51 11.857 -7.523 12.233 1.00 53.53 0.009 C ATOM 22 N THR A 52 10.527 -5.061 16.117 1.00 55.68 -0.344 N ATOM 23 HN THR A 52 10.475 -6.064 15.941 1.00 0.00 0.163 HD ]]></help> <citations> <citation type="doi">10.1002/jcc.21334</citation> </citations> </tool>