Mercurial > repos > bgruening > autodock_vina

annotate docking.xml @ 6:0ae768a0e5c0 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
author bgruening
date Wed, 19 Jun 2019 06:43:41 -0400
parents c410ffcabf9d
children 7b2f205b3f68
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6
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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1 <tool id="docking" name="Docking" version="0.2.1">
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2 <description>tool to perform protein-ligand docking with Autodock Vina</description>
2
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3 <requirements>
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4 <requirement type="package" version="1.1.2">autodock-vina</requirement>
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5 <requirement type="package" version="2.4.1">openbabel</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1" />
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9 </stdio>
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10 <command><![CDATA[
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11 #if $config_params.config_params == 'vals':
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12 vina
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13 --center_x '$config_params.center_x'
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14 --center_y '$config_params.center_y'
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15 --center_z '$config_params.center_z'
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16 --size_x '$config_params.size_x'
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17 --size_y '$config_params.size_y'
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18 --size_z '$config_params.size_z'
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19 --exhaustiveness '$config_params.exh'
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20 --num_modes 9999
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21 --energy_range 9999
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22 --receptor '$receptor'
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23 --ligand '$ligand'
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24 --out './output1.dat'
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25 --log './output2.dat'
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26 --cpu \${GALAXY_SLOTS:-1}
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27 #if $config_params.seed.seed == 'true':
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28 --seed '$config_params.seed.seed_value'
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29 #end if
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30 #end if
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31 #if $config_params.config_params == 'file':
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32 vina
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33 --config '$config_params.box'
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34 --receptor '$receptor'
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35 --ligand '$ligand'
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36 --out './output1.dat'
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37 --log './output2.dat'
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38 --cpu \${GALAXY_SLOTS:-1}
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39 #if $config_params.exh != "":
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40 --exhaustiveness $config_params.exh
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41 #end if
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42 #end if
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43 #if $output_format == 'sdf':
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44 && python '$__tool_directory__/convert_pdbqt_to_sdf.py' './output1.dat' '$sdf_output'
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45 #else
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46 && mv ./output1.dat '$file_output1'
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47 && mv ./output2.dat '$file_output2'
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48 #end if
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49
2
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50 ]]></command>
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51 <inputs>
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52 <param type="data" name="receptor" format="pdbqt" label="Receptor" help="Select a receptor (PDBQT format). This can be prepared using the receptor preparation tool." />
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53 <param type="data" name="ligand" format="pdbqt" label="Ligand" help="Select a ligand (PDBQT format). This can be prepared using the ligand preparation tool." />
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54 <conditional name="config_params">
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55 <param name="config_params" type="select" label="Specify parameters">
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56 <option value="file">Upload a config file to specify parameters</option>
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57 <option value="vals">Specify values directly</option>
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58 </param>
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59 <when value="vals">
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60 <param type="float" name="center_x" label="x coordinate" help="x coordinate of the binding site." value="0"/>
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61 <param type="float" name="center_y" label="y coordinate" help="y coordinate of the binding site." value="0"/>
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62 <param type="float" name="center_z" label="z coordinate" help="z coordinate of the binding site." value="0"/>
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63 <param type="float" name="size_x" label="x size" help="Length of the binding site (Å) in the x direction." value="0"/>
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64 <param type="float" name="size_y" label="y size" help="Length of the binding site (Å) in the y direction." value="0"/>
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65 <param type="float" name="size_z" label="z size" help="Length of the binding site (Å) in the z direction." value="0"/>
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66 <param type="integer" name="exh" label="Exhaustiveness" help="The number of poses to return from the docking job" value="10"/>
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67 <conditional name="seed">
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68 <param name="seed" type="boolean" label="Specify random seed for simulation reproducibility?"/>
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69 <when value="true">
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70 <param type="integer" name="seed_value" label="Random seed" help="Choose a seed value" value="1"/>
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71 </when>
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72 <when value="false"/>
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73 </conditional>
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74 </when>
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75 <when value="file">
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76 <param type="data" name="box" format="txt" label="Box configuration" help="Text file with the box configurations" />
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77 <param type="integer" name="exh" label="Exhaustiveness" help="The number of poses to return from the docking job (optional, will override any value specified in the config file)" optional="true"/>
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78 </when>
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79 </conditional>
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80 <param type="select" name="output_format" label="Output format" help="Select a format for the output files">
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81 <option value="pdbqt" selected="true">PDBQT (and separate log file with binding scores)</option>
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82 <option value="sdf">SDF</option>
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83 </param>
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84 </inputs>
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85 <outputs>
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86 <data name="file_output1" format="pdbqt">
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87 <filter>output_format == 'pdbqt'</filter>
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88 </data>
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89 <data name="file_output2" format="txt">
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90 <filter>output_format == 'pdbqt'</filter>
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91 </data>
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92 <data name="sdf_output" format="sdf">
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93 <filter>output_format == 'sdf'</filter>
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94 </data>
2
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95 </outputs>
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96 <tests>
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97 <test expect_num_outputs="2">
2
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98 <param name="receptor" value="3u1i_for_DM.pdbqt"/>
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99 <param name="ligand" value="NuBBE_1_obabel_3D.pdbqt"/>
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100 <param name="config_params" value="vals"/>
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101 <param name="center_x" value="70.92" />
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102 <param name="center_y" value="70.57" />
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103 <param name="center_z" value="36.86" />
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104 <param name="size_x" value="20.00" />
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105 <param name="size_y" value="18.40" />
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106 <param name="size_z" value="23.60" />
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107 <param name="seed" value="true" />
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108 <param name="seed_value" value="1" />
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109 <param name="exhaustiveness" value="10" />
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110 <param name="output_format" value="pdbqt" />
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111 <output name="file_output1" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt"/>
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112 <output name="file_output2" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.log"/>
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113 </test>
6
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114 <test expect_num_outputs="2">
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115 <param name="receptor" value="3u1i_for_DM.pdbqt"/>
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116 <param name="ligand" value="NuBBE_1_obabel_3D.pdbqt"/>
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117 <param name="config_params" value="file"/>
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118 <param name="box" value="config_complexo_dm.txt"/>
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119 <param name="output_format" value="pdbqt" />
2
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120 <output name="file_output1" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt"/>
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121 <output name="file_output2" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.log"/>
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122 </test>
6
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123 <test expect_num_outputs="1">
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124 <param name="receptor" value="3u1i_for_DM.pdbqt"/>
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125 <param name="ligand" value="NuBBE_1_obabel_3D.pdbqt"/>
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126 <param name="config_params" value="file"/>
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127 <param name="box" value="config_complexo_dm.txt"/>
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128 <param name="output_format" value="sdf" />
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129 <output name="sdf_output" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.sdf" lines_diff="40"/>
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130 </test>
2
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131 </tests>
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132 <help><![CDATA[
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133
5
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134 This tool performs protein-ligand docking using the Autodock Vina program.
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135
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136 -----
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137
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138 .. class:: infomark
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139
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140 **Inputs**
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141
5
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142 The first two inputs required are files (in the pdbqt format) describing the receptor and ligand respectively. These files are produced by the receptor and ligand preparation tools.
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143
5
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144 In addition, parameters for docking must be defined. The Cartesian coordinates of the center of the binding site should be provided, along with the size of the binding site along each dimension. Effectively, this defines a cuboidal volume in which docking is performed. Alternatively, a config file can be uploaded containing this information - such a file can be generated from the box parameter calculation file.
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145
6
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146 A format for the output should also be selected: the available options are PDBQT or SDF.
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147
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148 -----
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149
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150 .. class:: infomark
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151
4
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152 **Outputs**
2
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153
6
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154 Either PDBQT or SDF may be selected as output.
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155
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156 **Option 1: SDF**
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157
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158 An SDF file is produced as output. The binding affinity scores are also contained within the SDF file.::
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159
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160 OpenBabel06171915303D
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161
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
162 23 23 0 0 0 0 0 0 0 0999 V2000
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
163 66.9030 73.3450 36.0040 O 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
164 66.8190 73.2170 37.2120 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
165 66.0490 72.3370 37.8940 O 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
166 66.2290 70.9500 37.5970 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
167 67.2070 70.4140 38.6010 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
168 68.5140 70.1440 38.3980 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
169 69.2150 70.3400 37.0800 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
170 69.3810 69.5970 39.5210 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
171 68.7730 69.8280 40.9100 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
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172 69.3750 71.0120 41.6220 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
173 68.7550 72.1570 41.9760 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
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174 67.3280 72.4970 41.6430 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
175 69.4770 73.2270 42.7560 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
176 67.5570 74.0540 38.1920 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
177 66.9010 75.0480 38.9340 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
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178 67.6300 75.8170 39.8300 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
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179 68.9950 75.5990 39.9980 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
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180 69.6510 74.6060 39.2850 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
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181 68.9300 73.8240 38.3800 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
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182 67.0450 76.8040 40.5760 O 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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183 67.5560 77.4980 40.9760 H 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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parents: 5
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184 69.7010 76.3670 40.8780 O 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
185 69.2520 76.7930 41.5990 H 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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parents: 5
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186 1 2 2 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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187 2 3 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
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188 2 14 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
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189 4 3 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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parents: 5
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190 4 5 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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parents: 5
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191 6 5 2 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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parents: 5
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192 6 8 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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parents: 5
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193 7 6 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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parents: 5
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194 8 9 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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parents: 5
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195 9 10 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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parents: 5
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196 10 11 2 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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parents: 5
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197 11 13 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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parents: 5
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198 12 11 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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199 14 19 2 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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parents: 5
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200 14 15 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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parents: 5
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201 15 16 2 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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parents: 5
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202 16 17 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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parents: 5
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203 16 20 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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parents: 5
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204 17 22 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
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205 18 17 2 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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parents: 5
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206 19 18 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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parents: 5
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207 20 21 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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208 22 23 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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209 M END
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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210 > <MODEL>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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211 1
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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212
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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213 > <REMARK>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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214 VINA RESULT: 0.0 0.000 0.000
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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215 9 active torsions:
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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216 status: ('A' for Active; 'I' for Inactive)
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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217 1 A between atoms: C_2 and O_3
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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218 2 A between atoms: C_2 and C_14
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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219 3 A between atoms: O_3 and C_4
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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220 4 A between atoms: C_4 and C_5
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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221 5 A between atoms: C_6 and C_8
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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222 6 A between atoms: C_8 and C_9
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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223 7 A between atoms: C_9 and C_10
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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224 8 A between atoms: C_16 and O_17
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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225 9 A between atoms: C_19 and O_20
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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226
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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227 > <TORSDO>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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228 F 9
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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229
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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230 > <SCORE>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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231 0.0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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232
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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233 > <RMSD_LB>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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234 0.000
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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235
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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236 > <RMSD_UB>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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237 0.000
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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238
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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239
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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240 **Option 2: PDBQT**
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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241
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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242 Two outputs are generated if PDBQT output is selected. The first is another pdbqt file containing the molecular structure resulting from docking, such as the following example::
2
18dec59e29ae planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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243
4
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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244 MODEL 1
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245 REMARK VINA RESULT: -0.0 0.000 0.000
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246 REMARK 9 active torsions:
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247 REMARK status: ('A' for Active; 'I' for Inactive)
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248 REMARK 1 A between atoms: C_2 and O_3
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249 REMARK 2 A between atoms: C_2 and C_14
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250 REMARK 3 A between atoms: O_3 and C_4
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251 REMARK 4 A between atoms: C_4 and C_5
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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252 REMARK 5 A between atoms: C_6 and C_8
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253 REMARK 6 A between atoms: C_8 and C_9
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254 REMARK 7 A between atoms: C_9 and C_10
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255 REMARK 8 A between atoms: C_16 and O_17
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256 REMARK 9 A between atoms: C_19 and O_20
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257 ROOT
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258 ATOM 1 O LIG d 1 72.801 71.157 37.352 0.00 0.00 -0.259 OA
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259 ATOM 2 C LIG d 1 73.413 72.112 37.794 0.00 0.00 0.293 C
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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260 ENDROOT
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261 BRANCH 2 3
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262 ATOM 3 O LIG d 1 72.912 73.321 38.144 0.00 0.00 -0.314 OA
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263 BRANCH 3 4
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264 ATOM 4 C LIG d 1 71.868 73.332 39.120 0.00 0.00 0.206 C
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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265 BRANCH 4 5
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266 ATOM 5 C LIG d 1 72.522 73.555 40.453 0.00 0.00 0.002 C
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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267 ATOM 6 C LIG d 1 72.762 72.629 41.405 0.00 0.00 -0.085 C
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268 ATOM 7 C LIG d 1 72.390 71.176 41.274 0.00 0.00 0.043 C
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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269 BRANCH 6 8
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270 ATOM 8 C LIG d 1 73.435 73.012 42.714 0.00 0.00 0.037 C
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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271 BRANCH 8 9
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272 ATOM 9 C LIG d 1 74.184 74.348 42.631 0.00 0.00 0.031 C
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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273 BRANCH 9 10
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274 ATOM 10 C LIG d 1 75.668 74.175 42.431 0.00 0.00 -0.024 C
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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275 ATOM 11 C LIG d 1 76.399 74.547 41.360 0.00 0.00 -0.091 C
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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276 ATOM 12 C LIG d 1 75.833 75.151 40.104 0.00 0.00 0.042 C
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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277 ATOM 13 C LIG d 1 77.897 74.373 41.339 0.00 0.00 0.042 C
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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278 ENDBRANCH 9 10
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279 ENDBRANCH 8 9
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280 ENDBRANCH 6 8
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281 ENDBRANCH 4 5
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282 ENDBRANCH 3 4
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283 ENDBRANCH 2 3
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284 BRANCH 2 14
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285 ATOM 14 C LIG d 1 74.882 72.132 38.012 0.00 0.00 0.042 A
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286 ATOM 15 C LIG d 1 75.732 72.845 37.153 0.00 0.00 0.057 A
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287 ATOM 16 C LIG d 1 77.101 72.826 37.385 0.00 0.00 0.099 A
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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288 ATOM 17 C LIG d 1 77.623 72.116 38.462 0.00 0.00 0.098 A
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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289 ATOM 18 C LIG d 1 76.791 71.422 39.330 0.00 0.00 0.040 A
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290 ATOM 19 C LIG d 1 75.412 71.432 39.110 0.00 0.00 0.020 A
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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291 BRANCH 16 20
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292 ATOM 20 O LIG d 1 77.978 73.498 36.578 0.00 0.00 -0.358 OA
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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293 ATOM 21 HO LIG d 1 77.680 74.093 35.900 1.00 0.00 0.217 HD
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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294 ENDBRANCH 16 20
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295 BRANCH 17 22
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296 ATOM 22 O LIG d 1 78.971 72.100 38.675 0.00 0.00 -0.358 OA
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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297 ATOM 23 HO LIG d 1 79.541 71.651 38.060 1.00 0.00 0.217 HD
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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298 ENDBRANCH 17 22
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299 ENDBRANCH 2 14
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300 TORSDOF 9
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301 ENDMDL
2
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302
5
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303 The second output is a log file containing the binding affinity scores, like the following::
2
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304
4
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305 -----------------------------------------------------------------
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306 If you used AutoDock Vina in your work, please cite:
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307
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308 O. Trott, A. J. Olson,
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309 AutoDock Vina: improving the speed and accuracy of docking
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310 with a new scoring function, efficient optimization and
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311 multithreading, Journal of Computational Chemistry 31 (2010)
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312 455-461
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313
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314 DOI 10.1002/jcc.21334
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315
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316 Please see http://vina.scripps.edu for more information.
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317 ------------------------------------------------------------------
2
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318
4
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319 Reading input ... done.
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320 Setting up the scoring function ... done.
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321 Analyzing the binding site ... done.
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322 Using random seed: 1899908181
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323 Performing search ... done.
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324 Refining results ... done.
2
18dec59e29ae planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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325
4
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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326 mode | affinity | dist from best mode
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
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327 | (kcal/mol) | rmsd l.b.| rmsd u.b.
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
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328 -----+------------+----------+----------
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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329 1 -0.0 0.000 0.000
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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330 2 -0.0 2.046 2.443
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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331 3 -0.0 5.896 7.949
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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332 4 -0.0 2.518 3.100
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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333 5 -0.0 2.417 4.527
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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334 6 -0.0 5.686 7.689
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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335 7 -0.0 2.828 4.792
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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336 8 -0.0 5.547 7.086
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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337 9 -0.0 7.388 9.966
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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338 10 -0.0 7.877 11.352
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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339 11 -0.0 8.203 10.157
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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340 12 -0.0 5.163 7.653
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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341 13 -0.0 3.093 6.011
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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342 14 -0.0 7.998 11.146
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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343 15 -0.0 7.015 10.108
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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344 16 -0.0 8.795 11.682
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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345 17 -0.0 7.317 10.367
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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346 18 0.0 3.274 4.160
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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347 19 0.0 10.286 12.001
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 3
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348 20 0.0 3.566 5.349
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
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349 Writing output ... done.
2
18dec59e29ae planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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350 ]]></help>
18dec59e29ae planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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351 <citations>
18dec59e29ae planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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352 <citation type="doi">10.1002/jcc.21334</citation>
18dec59e29ae planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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353 </citations>
3
65ffed035ca8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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354 </tool>