ADL: directories

Steve Madden smadden at cumbrepharma.com
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
C:\Cygwin\usr\local\bin) 

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.

Steve

 

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