Mercurial > repos > bgruening > autodock_vina
view docking.xml @ 4:3c8e86318a81 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
| author | bgruening |
|---|---|
| date | Mon, 12 Feb 2018 04:23:13 -0500 |
| parents | 65ffed035ca8 |
| children | c410ffcabf9d |
line wrap: on
line source
<tool id="docking" name="Docking" version="0.1.0"> <description>Tool to running molecular docking with Autodock Vina</description> <requirements> <requirement type="package" version="1.1.2">autodock-vina</requirement> </requirements> <stdio> <exit_code range="1" /> </stdio> <command><![CDATA[ vina --config "$box" --receptor "$receptor" --ligand "$ligand" --out "$file_output1" --log "$file_output2" ]]></command> <inputs> <param type="data" name="box" format="txt" label="Box configuration" help="Select a text file with the box configurations" /> <param type="data" name="receptor" format="pdbqt" label="Receptor" help="Select a receptor PDBQT format. This can be prepared using the receptor preparation tool." /> <param type="data" name="ligand" format="pdbqt" label="Ligand" help="Select a ligand PDBQT format. This can be prepared using the ligand preparation tool." /> </inputs> <outputs> <data name="file_output1" format="pdbqt" /> <data name="file_output2" format="txt" /> </outputs> <tests> <test> <param name="box" value="config_complexo_dm.txt"/> <param name="receptor" value="3u1i_for_DM.pdbqt"/> <param name="ligand" value="NuBBE_1_obabel_3D.pdbqt"/> <output name="file_output1" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt"/> <output name="file_output2" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.log"/> </test> </tests> <help><![CDATA[ **What it does?** This tool performs molecular docking with Autodock Vina program. **Inputs** Three inputs are required for use this tools. The first is a text file with the box configurations, this file looks like the following example:: size_x = 20.00 size_y = 18.40 size_z = 23.60 center_x = 70.92 center_y = 70.57 center_z = 36.86 num_modes = 9999 energy_range = 9999 exhaustiveness = 10 cpu = 4 seed = 1 Where the parameters size_x, size_y, size_z, center_x, center_y and center_z are coordinates of the binding site. The parameters num_modes, energy_range, exhaustiveness, cpu and seed are autodock vina configurations to execute the algorithm. The second input is a receptor file (pdbqt) what is a output of the prepare receptor tool. The last input is a ligand file (pdbqt) what is a output of the prepare ligand tool. **Outputs** Two outputs are generated by this tool. The first is a pdbqt file with the molecule structure resulting of the molecular docking, this file looks like the following example:: MODEL 1 REMARK VINA RESULT: -0.0 0.000 0.000 REMARK 9 active torsions: REMARK status: ('A' for Active; 'I' for Inactive) REMARK 1 A between atoms: C_2 and O_3 REMARK 2 A between atoms: C_2 and C_14 REMARK 3 A between atoms: O_3 and C_4 REMARK 4 A between atoms: C_4 and C_5 REMARK 5 A between atoms: C_6 and C_8 REMARK 6 A between atoms: C_8 and C_9 REMARK 7 A between atoms: C_9 and C_10 REMARK 8 A between atoms: C_16 and O_17 REMARK 9 A between atoms: C_19 and O_20 ROOT ATOM 1 O LIG d 1 72.801 71.157 37.352 0.00 0.00 -0.259 OA ATOM 2 C LIG d 1 73.413 72.112 37.794 0.00 0.00 0.293 C ENDROOT BRANCH 2 3 ATOM 3 O LIG d 1 72.912 73.321 38.144 0.00 0.00 -0.314 OA BRANCH 3 4 ATOM 4 C LIG d 1 71.868 73.332 39.120 0.00 0.00 0.206 C BRANCH 4 5 ATOM 5 C LIG d 1 72.522 73.555 40.453 0.00 0.00 0.002 C ATOM 6 C LIG d 1 72.762 72.629 41.405 0.00 0.00 -0.085 C ATOM 7 C LIG d 1 72.390 71.176 41.274 0.00 0.00 0.043 C BRANCH 6 8 ATOM 8 C LIG d 1 73.435 73.012 42.714 0.00 0.00 0.037 C BRANCH 8 9 ATOM 9 C LIG d 1 74.184 74.348 42.631 0.00 0.00 0.031 C BRANCH 9 10 ATOM 10 C LIG d 1 75.668 74.175 42.431 0.00 0.00 -0.024 C ATOM 11 C LIG d 1 76.399 74.547 41.360 0.00 0.00 -0.091 C ATOM 12 C LIG d 1 75.833 75.151 40.104 0.00 0.00 0.042 C ATOM 13 C LIG d 1 77.897 74.373 41.339 0.00 0.00 0.042 C ENDBRANCH 9 10 ENDBRANCH 8 9 ENDBRANCH 6 8 ENDBRANCH 4 5 ENDBRANCH 3 4 ENDBRANCH 2 3 BRANCH 2 14 ATOM 14 C LIG d 1 74.882 72.132 38.012 0.00 0.00 0.042 A ATOM 15 C LIG d 1 75.732 72.845 37.153 0.00 0.00 0.057 A ATOM 16 C LIG d 1 77.101 72.826 37.385 0.00 0.00 0.099 A ATOM 17 C LIG d 1 77.623 72.116 38.462 0.00 0.00 0.098 A ATOM 18 C LIG d 1 76.791 71.422 39.330 0.00 0.00 0.040 A ATOM 19 C LIG d 1 75.412 71.432 39.110 0.00 0.00 0.020 A BRANCH 16 20 ATOM 20 O LIG d 1 77.978 73.498 36.578 0.00 0.00 -0.358 OA ATOM 21 HO LIG d 1 77.680 74.093 35.900 1.00 0.00 0.217 HD ENDBRANCH 16 20 BRANCH 17 22 ATOM 22 O LIG d 1 78.971 72.100 38.675 0.00 0.00 -0.358 OA ATOM 23 HO LIG d 1 79.541 71.651 38.060 1.00 0.00 0.217 HD ENDBRANCH 17 22 ENDBRANCH 2 14 TORSDOF 9 ENDMDL The last is a log file with the binding affinity scores, this file looks like the following example:: ----------------------------------------------------------------- If you used AutoDock Vina in your work, please cite: O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461 DOI 10.1002/jcc.21334 Please see http://vina.scripps.edu for more information. ------------------------------------------------------------------ Reading input ... done. Setting up the scoring function ... done. Analyzing the binding site ... done. Using random seed: 1899908181 Performing search ... done. Refining results ... done. mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- 1 -0.0 0.000 0.000 2 -0.0 2.046 2.443 3 -0.0 5.896 7.949 4 -0.0 2.518 3.100 5 -0.0 2.417 4.527 6 -0.0 5.686 7.689 7 -0.0 2.828 4.792 8 -0.0 5.547 7.086 9 -0.0 7.388 9.966 10 -0.0 7.877 11.352 11 -0.0 8.203 10.157 12 -0.0 5.163 7.653 13 -0.0 3.093 6.011 14 -0.0 7.998 11.146 15 -0.0 7.015 10.108 16 -0.0 8.795 11.682 17 -0.0 7.317 10.367 18 0.0 3.274 4.160 19 0.0 10.286 12.001 20 0.0 3.566 5.349 Writing output ... done. ]]></help> <citations> <citation type="doi">10.1002/jcc.21334</citation> </citations> </tool>