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Frequently Asked Questions (& Answers!)

Running ADT

How do I set the AutoDock/AutoGrid Path in ADT?

How do I make ADT remember the path to AutoDock and AutoGrid executables?

The easiest way is to edit the file from the AutoDockTools folder and replace autogrid3/autodock3.

hostMacros = {
'localhost': { 'host' : 'localhost',
'autogrid' : 'autogrid3', # replace autogrid3 with autogrid4 path
'autodock' : 'autodock3', # replace autodock3 with autodock4 path
'queuetype' : 'int',
'userSpecific' : 0 },

The problem with this approach is that when you update ADT using Help->Update menu, you need to redo this for the updated as well. The other way to make ADT remember the path is to create a file called _adtrc in the current working directory and paste the following code in there:

import socket
localhost = socket.gethostbyname_ex(socket.gethostname())[0]
self.ADstart_editHostMacros.addItem_cb(macro=localhost, host=localhost,autogrid='autogrid4',autodock='autodock4',queuetype='int',userSpecific=0)

Since ADT runs _adtrc when it starts up, this approach should survive across updates.

This FAQ applies to: AutoDock 3, AutoDock 4

Where should I start ADT?

If I want to start ADT from the UNIX/Linux/Mac OS X command line, where should I start it?

You should always start ADT in the same directory as the macromolecule and ligand files you want to dock. You can start ADT from the command line in a Terminal by typing “adt” and pressing <Return> or <Enter>.
by morris last modified 2007-07-19 17:31
Contributors: Ruth Huey, Garrett M. Morris, Sargid Dallakyan, Stefano Forli

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