ADL: Get the ligand information from dlg using AutoDock4

Tee Pioj tee_piorj at yahoo.com
Sat Jan 5 06:04:32 PST 2008


Hi!
Your problem need setting environment variable. If you use bash shell, try following:
In your home dir, type vi .bashrc and then copy these lines

PATH=/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:$AUTODOCK_UTI:$AUTODOCK_BIN:$AUTODOCK_HOME
AUTODOCK_BIN=/your_binary_dir_autodock (e.g. /usr/local/bin)
AUTODOCK_UTI=/your_autodock_share_dir (e.g. /usr/local/dist305/src/)
AUTODOCK_HOME=/your_autodock_dir (e.g. /usr/local/dist305/)
 
export PATH
export AUTODOCK_HOME
export AUTODOCK_BIN
export AUTODOCK_UTI

type wq! to save and exit
type source .bashrc (twice)

type echo $PATH to check that usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:$AUTODOCK_UTI:$AUTODOCK_BIN:$AUTODOCK_HOME appear in the line.

try to use get-docked again, it should work
Good luck

----- Original Message ----
From: Hao Tang <haotang1982 at gmail.com>
To: autodock at scripps.edu
Sent: Saturday, January 5, 2008 3:59:52 AM
Subject: ADL: Get the ligand information from dlg using AutoDock4

Hello,
I am a new user for AutoDock4. I have successfully generate the dlg file 
by using the ADT. And I can also visualize the docked molecules using 
ADT. But I want to extract the docked ligands in pdb format or (mol2, 
etc.) from the dlg file . Do anyone know how to do it?  I tried to use 
"get-docked  result.dlg " command, but it doesn't work. The system does 
not recognize get-docked command.

Thank you very much in advance.

Hao
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