Mercurial > repos > bgruening > autodock_vina_prepare_ligand
view prepare_ligand.xml @ 2:f6eb53a200df draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
| author | bgruening |
|---|---|
| date | Tue, 07 May 2019 13:32:15 -0400 |
| parents | 1b4a6ebd9898 |
| children | 50871000e977 |
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<tool id="prepare_ligand" name="Prepare ligand" version="0.1.0"> <description>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 $ligand ./ligand.mol2 && prepare_ligand4.py -l ./ligand.mol2 -v -o "$file_output" -U nphs_lps -A hydrogens ]]></command> <inputs> <param type="data" name="ligand" format="mol2" label="The ligand which needs to be prepared" help="In MOL2 format." /> </inputs> <outputs> <data name="file_output" format="pdbqt" /> </outputs> <tests> <test> <param name="ligand" value="NuBBE_1_obabel_3D.mol2"/> <output name="file_output" file="NuBBE_1_obabel_3D.pdbqt"/> </test> </tests> <help><![CDATA[ .. class:: infomark **What this tool does** This tool uses the MGLTools programming package to convert a mol2 molecule file to a pdbqt molecule file, which the Autodock Vina program uses to perform molecular docking. The output file has a similar format to the pdb input, with atom types modified to conform to AutoDock atom types and an extra column containing Gasteiger charges added. ----- .. class:: infomark **Input** A mol2 file is required to use this tool. * Example:: @<TRIPOS>MOLECULE NuBBE_1 21 21 0 0 0 SMALL GASTEIGER @<TRIPOS>ATOM 1 O -0.9469 -0.4359 -3.2099 O.2 1 LIG1 -0.2449 2 C -1.2069 0.2449 -2.2351 C.2 1 LIG1 0.3396 3 O -1.9353 -0.1138 -1.1515 O.3 1 LIG1 -0.4570 4 C -2.3385 -1.4828 -1.0650 C.3 1 LIG1 0.1113 5 C -1.7447 -2.0319 0.2001 C.2 1 LIG1 -0.0480 6 C -0.5501 -2.6439 0.3381 C.2 1 LIG1 -0.0731 7 C 0.4046 -2.8855 -0.8015 C.3 1 LIG1 -0.0437 8 C -0.0862 -3.1529 1.6937 C.3 1 LIG1 -0.0285 9 C 0.7304 -2.1137 2.4728 C.3 1 LIG1 -0.0308 10 C 1.1870 -2.6184 3.8183 C.2 1 LIG1 -0.0850 11 C 2.3521 -3.2333 4.1099 C.2 1 LIG1 -0.0796 12 C 3.4007 -3.6048 3.0986 C.3 1 LIG1 -0.0440 13 C 2.6989 -3.6136 5.5272 C.3 1 LIG1 -0.0440 14 C -0.7776 1.6572 -2.0661 C.ar 1 LIG1 0.0627 15 C -0.6402 2.2240 -0.7903 C.ar 1 LIG1 -0.0026 16 C -0.2486 3.5509 -0.6768 C.ar 1 LIG1 0.1590 17 O -0.1045 4.1587 0.5397 O.3 1 LIG1 -0.5033 18 C 0.0124 4.3080 -1.8161 C.ar 1 LIG1 0.1583 19 O 0.3891 5.6141 -1.6913 O.3 1 LIG1 -0.5033 20 C -0.1020 3.7535 -3.0825 C.ar 1 LIG1 -0.0158 21 C -0.4936 2.4191 -3.2122 C.ar 1 LIG1 -0.0441 @<TRIPOS>BOND 1 1 2 2 2 2 3 1 3 3 4 1 4 4 5 1 5 5 6 2 6 6 7 1 7 6 8 1 8 8 9 1 9 9 10 1 10 10 11 2 11 11 12 1 12 11 13 1 13 2 14 1 14 14 15 ar 15 15 16 ar 16 16 17 1 17 16 18 ar 18 18 19 1 19 18 20 ar 20 20 21 ar 21 14 21 ar ----- .. class:: infomark **Output** The output is a pdbqt molecule file. * Example:: 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 -0.947 -0.436 -3.210 0.00 0.00 -0.259 OA ATOM 2 C LIG d 1 -1.207 0.245 -2.235 0.00 0.00 0.293 C ENDROOT BRANCH 2 3 ATOM 3 O LIG d 1 -1.935 -0.114 -1.151 0.00 0.00 -0.314 OA BRANCH 3 4 ATOM 4 C LIG d 1 -2.338 -1.483 -1.065 0.00 0.00 0.206 C BRANCH 4 5 ATOM 5 C LIG d 1 -1.745 -2.032 0.200 0.00 0.00 0.002 C ATOM 6 C LIG d 1 -0.550 -2.644 0.338 0.00 0.00 -0.085 C ATOM 7 C LIG d 1 0.405 -2.885 -0.801 0.00 0.00 0.043 C BRANCH 6 8 ATOM 8 C LIG d 1 -0.086 -3.153 1.694 0.00 0.00 0.037 C BRANCH 8 9 ATOM 9 C LIG d 1 0.730 -2.114 2.473 0.00 0.00 0.031 C BRANCH 9 10 ATOM 10 C LIG d 1 1.187 -2.618 3.818 0.00 0.00 -0.024 C ATOM 11 C LIG d 1 2.352 -3.233 4.110 0.00 0.00 -0.091 C ATOM 12 C LIG d 1 3.401 -3.605 3.099 0.00 0.00 0.042 C ATOM 13 C LIG d 1 2.699 -3.614 5.527 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 -0.778 1.657 -2.066 0.00 0.00 0.042 A ATOM 15 C LIG d 1 -0.640 2.224 -0.790 0.00 0.00 0.057 A ATOM 16 C LIG d 1 -0.249 3.551 -0.677 0.00 0.00 0.099 A ATOM 17 C LIG d 1 0.012 4.308 -1.816 0.00 0.00 0.098 A ATOM 18 C LIG d 1 -0.102 3.753 -3.083 0.00 0.00 0.040 A ATOM 19 C LIG d 1 -0.494 2.419 -3.212 0.00 0.00 0.020 A BRANCH 16 20 ATOM 20 O LIG d 1 -0.104 4.159 0.540 0.00 0.00 -0.358 OA ATOM 21 HO LIG d 1 0.164 5.067 0.617 1.00 0.00 0.217 HD ENDBRANCH 16 20 BRANCH 17 22 ATOM 22 O LIG d 1 0.389 5.614 -1.691 0.00 0.00 -0.358 OA ATOM 23 HO LIG d 1 0.567 6.131 -2.469 1.00 0.00 0.217 HD ENDBRANCH 17 22 ENDBRANCH 2 14 TORSDOF 9 ]]></help> <citations> <citation type="doi">10.1002/jcc.21334</citation> </citations> </tool>