Subject: get-dockings command in autodock problems

From: "will" <ewlowe(at)helios.acomp.usf.edu>
Date: Fri, 9 Jul 2004 18:58:44 -0400

Upon giving this command, I get the following error:
 
Sed: can't open fixatomnames.sed  (can't find file or directory)
 
The file is in the same folder that the 'get-dockings' command is in, so
I'm not sure how it can 'not find' the file.  Also, the prepare command
mentioned in the autodock manual doesn't seem to exist in my
distribution.  Prepare-gpf+dpf works fine, but 'prepare m s' where m is
macro and s substrate doesn't seem to be on my computer.  Job3 gives the
error:
 
Autodock_uti:  undefined variable
 
While job gives:
 
Autodock_root:  undefined variable
 
Unfortunately, I have no real experience with linux and am not sure how
to fix these problems.  I tried the "setenv. " and "set path=$path
$autodock_uti" as mentioned in the manual, but I don't even know if that
has anything to do with the problems I'm experiencing now.  I'm running
cygwin on windows xp in case that's pertinent.  Thanks for the help in
advance.
 
Will
University of South Florida
Department of Chemistry and Biochemistry