[Dock-fans] What does Dock 5.0 give in terms of results?

Terry Lang terry at cgl.ucsf.edu
Wed Apr 13 17:36:58 PDT 2005


Dear Sam,

   First of all, there is something wrong with your DOCK run.  The value 
you should get from the demo should be around -32 for Energy score.  It is 
not clear why you would get the negative infinity result from what you have 
here, but as a guess, make sure you have the MPI library installed in 
addition to Cygwin.  Did you get any other errors when you were running the 
demo?
   In answer to your question, when DOCK works properly, it will create a 
file in .mol2 format.  There are several free programs available to 
visualize this format. If you have a particular pdb viewer in mind, you 
should be able to convert from .mol2 format to .pdb format using the 
program babel.  For more information on both the visualization programs and 
on babel, go to http://dock.compbio.ucsf.edu/DOCK_Links/index.htm.

Sincerely,
Terry


At 09:28 PM 4/12/2005, you wrote:
>Dear all users,
>I am new to Dock program.  May someone answer me "what can I get out of
>dock?"  I just ran tutorial included in the installation file, and what
>I got from the output file was the following, (I just attached the
>results)
>
>-----------------------------------
>Molecule: UNNAMED
>
>  Anchors:               1
>  Orientations:          500
>  Conformations:         45
>
>  Energy Score:           -1.INF00
>           vdw:           -1.INF00
>            es:-87353961318052317000000000000000000.000000
>
>
>
>1 Molecules Processed
>Elapsed time:   98.296 seconds
>
>Since I am using windows xp, and I installed cygwin for this process.
>i would like to know is there an output pdb file that i can visualize
>the result in a pdb viewer? And if not, how can I generate one so that
>I can visualize them?
>
>
>
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P. Therese (Downing) Lang
Kuntz and James Labs
UCSF - CCB Graduate Program
Phone:  (415)476-3986




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