Mercurial > repos > bgruening > autodock_vina
diff 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 |
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--- a/docking.xml Sat Jun 04 12:36:59 2016 -0400 +++ b/docking.xml Mon Feb 12 04:23:13 2018 -0500 @@ -28,142 +28,142 @@ </test> </tests> <help><![CDATA[ - ** What it does? ** +**What it does?** - This tool performs molecular docking with Autodock Vina program. +This tool performs molecular docking with Autodock Vina program. - ** inputs ** +**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: +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 + 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. +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. +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 ** +**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: +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 + 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: +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. - ------------------------------------------------------------------ + ----------------------------------------------------------------- + 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. + 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. + 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>