Before launching AutoGrid/AutoDock, make sure that you have AutoDock installed as described in:

• How do I install AutoDock on Windows?

• How do I install AutoDock on Linux and Mac OS X?

Click on ADT → Run → Run AutoGrid... to open the widget shown below:

Replace autogrid3 with the full path for AutoGrid executable. Note that if the folder containing AutoDock executables is in your PATH environment variable, then you don't need to specify the full path (just replace autogrid3 with autogrid4 or autogrid4.exe if needed). Click Launch to execute command shown in the Cmd: box. Note that this command is executed in the current working directory.

Troubleshooting

Windows users:

If you are getting "'autogrid4.exe' is not recognized as an internal or external command", click on Browse for Program Pathname, locate autogrid4.exe on your file system and click Open. See also, DOS Lesson on Path, Environment Variables in Windows and Autodock for Windows.doc (27KB). Note that, input files don't necessarily need to be in the same folder with autogrid4.exe. They need to be, however, in the current working directory for autogrid4.exe to find them.If you are still unable to lunch autogrid4, please read Using AutoDock 4 with AutoDockTools for instruction on how to run autogrid4 from a command line.

Unix/Linux and Mac OS X users:

If Autodock Process Manager window flashes up and then disappears, this probably means that AutoDock terminated abnormally. Please copy/paste Cmd: string into command line interpreter to troubleshooting the problem.