4. Default settings

To modify the GriDock default  settings, you can edit the gridock.xml file in the ...\VEGA ZZ\Config directory by your preferred text editor. The following scheme shows the meaning of each Xml tag:

 

Configuration file   Description 
<gridock version="1.0">
      

Main tag:
- version -> Version number of the configuration file.

 
  <maxzipsize>4000000000</maxzipsize>
  

Maximum size in bytes of each zip file containing AutoDock output files. You must remember that it can't be greater than 4 Gb (4,294,967,296 bytes). If the file system is  FAT32, it's strongly recommended to set this parameter to 2000000000 in order to not exceed the 2,147,483,648 value that is the maximum file size supported by this file system.

 
  <writezip>true</writezip>
  

Enabling this flag, the output files generated by AutoDock 4 are stored in zip archives. The supported arguments are: on / off, yes / no, true / false.

 
  <ammp timeout="120">
  

AMMP settings:
- timeout is the maximum time in seconds that can be used by AMMP to finish the calculation.

 
    <to3d>
      use none bond angle torsion hybrid nonbon;
      setf mxdq 1.0;
      gsdg 15 0;
      steep 50 1;
      cngdel 3000 0 0.01;
   AMMP commands used to perform the 1D or 2D to 3D conversion. For more details, see the AMMP manual. 
    </to3d>
   End of 3D conversion section. 
  </ammp>
   End of AMMP settings. 
  <autodock timeout="12000"></autodock>
  

AutoDock 4 settings:
- timeout is the maximum time in seconds that can be used by AutoDock to finish the docking.

 
  <vega timeout="120">
  

VEGA  settings:
- timeout is the maximum time in seconds that can be used by VEGA to finish the calculation/conversion. 

    <charges>gasteiger</charges>
  

Atom charges attribution method. It can be one of the methods supported by VEGA or none if you don't need to assign the atom charges. See the -c option in the VEGA manual.

 
    <potential>autodock</potential>
  

Atom type template that must be one of the templates supported by VEGA. See the -p option in the VEGA manual.

 
    <torsions>flex</torsions>
  

Method to find torsions/dihedrals in the ligand structures. See the -j option in the VEGA manual.

 
  </vega>
  

End of VEGA settings.

 
  <csvout decsep="auto">
  

Comma Separated Values (CSV) settings:
- decsep can be auto to detect the locale settings for the decimal separator (this capability works with Windows only) or the decimal separator character (e.g. , or .).

 
    <delay>300</delay>
  

In order to avoid the file system overload, the write procedure of the output csv file is delayed of the specified number of second. Changing the value to zero (0), the write is done immediately and not delayed.

 
  </csvout>
   End of CSV settings. 
</gridock>
  

End of the GriDock configuration file.