ADL: directories

Roberta King bps691king at gmail.com
Tue Oct 16 07:43:17 PDT 2007


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
directories:

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

This is most important because AutoGrid4/AutoDock4 looks for PDBQT files in
the cwd. The cwd is also used for making ADT remember the path to Autodock
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 dpf/gpf
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 wrong.

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

I am using MGL Tools version 1.4.5, so I also tried the easier way of using
File->Preferences->Modify Defaults to change the startup directory. But as
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

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


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