ADL: directories

vijaya subramanian vijaya65 at
Tue Oct 16 07:55:36 PDT 2007

pwd tells you which directory you are in.  Run ADT from the directory where you have your pdb file. 
Don't chnage the preferences within MGL-tools.  When you launch autogrid be sure to include the path to autogrid.
You can use browse to set that up.
----------------------------------------> Date: Tue, 16 Oct 2007 10:43:17 -0400> From: bps691king at> 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> 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 "", line 1, in ?> os.getcwd()> NameError: name 'os' is not defined>>>> os.getcwd()> Traceback (most recent call last):> File "", 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> ________________________________________________> --- ADL: AutoDock List --- ---

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