ADL: Autodock shell scripts

Philip Crawford p.crawford at unsw.edu.au
Mon Jan 23 17:36:16 PST 2006


John,
I just checked the manual and it is on page 24. (I searched using Acrobat,
it's under a heading "Getting Started...")
I wonder if it would be possible for the AutoDock team to update the manual
with a cross-reference to this from the start of the instructions on the
actual scripts?
 
Cheers,
 
Phil
__________________________________________________
Philip Crawford, B. Comp. Sc., MIEEE
School of Medical Sciences
The University of NSW
Phone: +61-2-9385 2564
Mobile: +61-419-294 698
Fax: +61-2-9385 1059
Email: p.crawford at unsw.edu.au
__________________________________________________
 

  _____  

From: John Bruning [mailto:jbruning at scripps.edu] 
Sent: Tuesday, 24 January 2006 12:15 PM
To: Philip Crawford
Subject: RE: Autodock shell scripts



Thanks, that actually helps alot.  I didn't see that in their documentation
anywhere probably because it wasn't there :)


-----Original Message-----
From: Philip Crawford [mailto:p.crawford at unsw.edu.au]
Sent: Mon 1/23/2006 7:43 PM
To: John Bruning; autodock at scripps.edu
Subject: RE: Autodock shell scripts

John,
Hi. Your problem is that the scripts depend on an environment variable
AUTODOCK_UTI which should point to the share directory in which the scripts
reside. (Some scripts call other scripts as $AUTODOCK_UTI/...). If this
environment variable is not set, the script doesn't know where to look.

Unfortunately, I can't help you with how to set this in the C-shell. I'm
pretty sure that it should go in your .cshrc file but I'm not sure how.

Cheers,

Phil
__________________________________________________
Philip Crawford, B. Comp. Sc., MIEEE
School of Medical Sciences
The University of NSW
Phone: +61-2-9385 2564
Mobile: +61-419-294 698
Fax: +61-2-9385 1059
Email: p.crawford at unsw.edu.au
__________________________________________________

-----Original Message-----
From: autodock-bounces at scripps.edu [mailto:autodock-bounces at scripps.edu] On
Behalf Of John Bruning
Sent: Tuesday, 24 January 2006 8:56 AM
To: autodock at scripps.edu
Subject: ADL: Autodock shell scripts

Hi,
I am having trouble getting the autodock shell scripts to work.  I just want
a pdb file that other programs can recognize (such as quanta or coot),  So I
am using the get-dockings shell script.  It seems to start fine but then
crashes saying,

"Running columnclean on test.dlg.pdb
columnclean: Command not found.
Running fixatomnames on test.dlg.pdb
fixatomnames: Command not found."

The other scripts, columnclean and fixatoms are in the same directory, so
why does get-dockings choke with this error?

Also, I am using a tcsh shell in Redhat linux if that is important.  I also
get the problem in my Cygwin windows version.

I don't know why getting pdbs is so complicated, but is there another,
simpler way to get pdbs of the docked molecules that I am missing?


Thanks,
John Bruning




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