ADL: Autodock 4 Freezing

David Harrison david_harrison11 at hotmail.com
Wed Jun 6 04:09:40 PDT 2007


O.K. I've got everything working installed correctly on a windows platform.  
I can successfully perform autogrid, ADT freezes but eventually gets 
through.  When I trying running autodock it freezes totally.

This looks like the same problem below:

Do we know whether this has been fixed yet?  Also how do I "run autogrid4 in 
the cmd window"?



Starting with Version 1.4.5 you can also change the startup directory by 
using
File->Preferences->Modify Defaults menu. Scroll down till you see the 
Startup
Directory entry, change it and press make default.

Regarding ADT Not responding part, run autogrid4 in the cmd window without 
using
  ADT before we fix the problem.

Thanks,
Sargis

Savani Anbalagan wrote:
>hi thanx a lot..
>
>but now another problem..
>
>i was goin thro the tutorial...  hsp1 with ind
>
>
>when i run autogrid4, ADT gets stuck.....
>
>in the cmd window
>
>
>"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
>        _______________________________________________________
>
>__________//____________________________/////_________________/________
>_________/__/____________/_____________/______________/_______/________
>________/____/___________/_____________/______________________/________
>________/____/__/_____/_/////___/////__/__////_/_///__/__////_/________
>_______/______/_/_____/__/_____/_____/_/_____/_//___/_/_/____//________
>_______////////_/_____/__/_____/_____/_/_____/_/______/_/_____/________
>_______/______/_/____//__/___/_/_____/_/_____/_/______/_/____//________
>_______/______/__////_/___///___/////___/////__/______/__////_/________
>
>        _______________________________________________________
>
>                                 ______
>                                /      \
>                               /        \
>                              /          \
>                              \    /\    /
>                               \  /  \  /
>                                \/ /\ \/
>                                  /  \
>                                 /____\
>
>
>                 ______________________________________
>                |                                      |
>                |            AutoGrid 4.00             |
>                |                                      |
>                |        Garrett M. Morris, TSRI       |
>                |            Ruth Huey, TSRI           |
>                |        David S. Goodsell, TSRI       |
>                |         Arthur J. Olson, TSRI        |
>                |                                      |
>                |        (c) 1989-2005, TSRI           |
>                |   The Scripps Research Institute     |
>                |______________________________________|
>
>                 ______________________________________
>                |                                      |
>                | Calculation of van der Waals, H-Bond,|
>                |   Electrostatic Potential Energy, &  |
>                |   Desolvation Free Energy Grid Maps  |
>                |             for AutoDock             |
>                |______________________________________|
>
>
>
>
>
>                            $Revision: 1.54 $
>
>
>
>Maximum number of maps that can be computed = 22 (defined by MAX_MAPS in
>"autoco
>mm.h").
>
>
>This file was created at:                       9:20 10" p.m., 05/25/2007
>                    using:                       "mohan"
>
>
>Setting up parameter library with factory defaults.
>
>
>Free energy coefficient for the van der Waals term =    0.1560
>
>Free energy coefficient for the H-bonding term     =    0.0974
>
>Free energy coefficient for the electrostatic term =    0.1465
>
>Free energy coefficient for the desolvation term   =    0.1159
>
>Free energy coefficient for the torsional term     =    0.2744
>
>Parameters for the atom type named "H" were read in from the parameter
>library a
>s follows:
>         R-eqm = 2.00 Angstrom,  weighted epsilon = 0.003,  At.frag.vol. =
>0.000,
>   At.solv.par. = 0.001,
>         Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type = 0,  
>bond
>inde
>x = 3
>
>
>
>
>         Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type = 0,  
>bond
>inde
>x = 4
>
>Parameters for the atom type named "Zn" were read in from the parameter
>library
>as follows:
>         R-eqm = 1.48 Angstrom,  weighted epsilon = 0.086,  At.frag.vol. =
>1.700,
>   At.solv.par. = -0.001,
>         Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type = 0,  
>bond
>inde
>x = 4
>
>Parameters for the atom type named "ZN" were read in from the parameter
>library
>as follows:
>         R-eqm = 1.48 Angstrom,  weighted epsilon = 0.086,  At.frag.vol. =
>1.700,
>   At.solv.par. = -0.001,
>         Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type = 0,  
>bond
>inde
>x = 4
>
>Parameters for the atom type named "Br" were read in from the parameter
>library
>as follows:
>         R-eqm = 4.33 Angstrom,  weighted epsilon = 0.061,  At.frag.vol. =
>42.566
>,  At.solv.par. = -0.001,
>         Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type = 0,  
>bond
>inde
>x = 4
>
>Parameters for the atom type named "BR" were read in from the parameter
>library
>as follows:
>         R-eqm = 4.33 Angstrom,  weighted epsilon = 0.061,  At.frag.vol. =
>42.566
>,  At.solv.par. = -0.001,
>         Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type = 0,  
>bond
>inde
>x = 4
>
>Parameters for the atom type named "I" were read in from the parameter
>library a
>s follows:
>         R-eqm = 4.72 Angstrom,  weighted epsilon = 0.086,  At.frag.vol. =
>55.059
>,  At.solv.par. = -0.001,
>         Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type = 0,  
>bond
>inde
>x = 4
>
>ha
>
>
>
>"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
>
>if i try end task by ctrl+alt+del
>
>it shows ADT Not responding
>
>
>dono wat to do..
>
>please help..
>
>Thanx
>
>
>A.SAVANI
>IVyr Integrated M.Tech. Industrial Biotechnology
>SASTRA University
>Thanjavur
>India
>
>
>
>
>
>
>
>
>On 25/05/07, Philip Crawford <p.crawford at unsw.edu.au> wrote:
>
>>If you create a shortcut to runadt.py, copy it to the directory where
>>your molecule files are and simply double-click it in Windows Explorer,
>>you should start ADT.
>>
>>To have ADT launch Autogrid and Autodock jobs, you need the following 3
>>files in a directory on the standard Windows PATH:
>>autodock4.exe
>>autogrid4.exe
>>cygwin1.dll
>>
>>I personally prefer to create a C:\ADT\bin directory and put those files
>>in there. Then I add the C:\ADT\bin directory to the path. An
>>alternative is to put the files in a directory which is already on the
>>path.
>>
>>Phil Crawford
>>
>>Savani Anbalagan wrote:
>>
>>>Hi all..
>>>
>>>I have Windows XP.. I have installed cygwin, python 2.4 and ADT 1.4.5(in
>>>default installion folders)
>>>from windows prompt, i am able to run ADT..
>>>
>>>but How to start ADT from the folder which has receptor and ligand?
>>>
>>>in cygwin window
>>>
>>>
>>>if i try
>>>c:/python24/python c:/program\ files/mgltools 1.4.5
>>>/mgltoolspckgs/autodocktools/bin/runadt.py
>>>
>>>it says c:/python24/python: can't open file 'c:/program files/mgltools':
>>>[Errno 2] No such file or directory
>>>
>>>
>>>please help....
>>>
>>>A.SAVANI
>>>IVyr Integrated M.Tech. Industrial Biotechnology
>>>SASTRA University
>>>Thanjavur
>>>India
>>>________________________________________________
>>>--- ADL: AutoDock List  ---
>>
>>http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>>
>>>
>>>
>>
>>
>
>

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