ADL: directories

Steve Madden smadden at
Tue Oct 16 08:11:29 PDT 2007

I have not set it up to be able to run the commands through the ADT
interface but here is what I have done to run these from a cygwin
window. So that I don't have to include the full path every time, I
placed the executable files (autogrid4.exe and autodock4.exe) in the
cygwin usr\local\bin directory (which on my system is

Once I have created the pdbqt files and dpf/gpf files in ADT, I open a
cygwin window and navigate to the directory that contains these files.
Once I am in the directory, I start the autogrid/autodock process using
the command "autogrid4 -p mygrid.gpf -l mygridlog.glg" or "autodock4 -p
mydock.dpf -l mydocklog.dlg"

Hope this helps.



-----Original Message-----
From: autodock-bounces at [mailto:autodock-bounces at]
On Behalf Of Roberta King
Sent: Tuesday, October 16, 2007 9:43 AM
To: autodock at
Subject: ADL: directories

My colleagues and I are struggling with what may be very simple UNIX
concepts, but which are very difficult for Windows users. The issue is

Current working directory (cwd) vs. startup directory vs. default

This is most important because AutoGrid4/AutoDock4 looks for PDBQT files
the cwd. The cwd is also used for making ADT remember the path to
and Audogrid executables. (As I have learned from FAQs on the website.)

Autodock Tools runs for me, I can prepare PDBQT files, I can prepare
files, but when I launch autogrid or autodock nothing happens because it
cannot find the .pdbqt files nor .map files. (Actually searching my hard
drive finds no .map files at all!). Obviously I am doing something

When I try to learn my cwd, this is what happens.....
Traceback (most recent call last):
  File "<pyshell#1>", line 1, in ?
NameError: name 'os' is not defined
>>> os.getcwd()
Traceback (most recent call last):
  File "<pyshell#4>", line 1, in ?
NameError: name 'os' is not defined

I am using MGL Tools version 1.4.5, so I also tried the easier way of
File->Preferences->Modify Defaults to change the startup directory. But
far as I understand from the description, this changes the startup
directory, but not the current working directory (???).

Please help a suffering Windows user.

Thank you.

Roberta S. King, Ph.D.
Department of Biomedical and Pharmaceutical Sciences
College of Pharmacy
University of Rhode Island
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