[Dock-fans] Doubt about Zinc based active sites

Terry Lang terry at cgl.ucsf.edu
Mon Jul 11 15:04:17 PDT 2005

Dear Arvind,

          It looks like from the error messages you are getting that you 
are using DOCK 4.  Parameters for zinc were not introduced until DOCK 
5.  If you need to model a zinc receptor, I would recommend downloading 
a new version of the software. 
          If you have a reason to use version 4 over 5, you can add the 
zinc parameter to the vdw file manually.  We would typically use the 
values below.  However, so you know, the output you are getting is for 
chemical screening assignment.  There is more information about how to 
add zinc to chemical scoring and screening in the DOCK 4 manual.


radius   1.10
well_depth      0.0125

Arvind Ramanathan wrote:

>As I was trying to dock a molecule into thermolysin, I observed that it
>was not docking correctly to the protein. Hence, I looked at the various
>steps, and found that when grid is run, I get the following output (in
>verbose mode):
>Chemical Assignment
>  4698    C   C.2   null
>  4699    O O.co2   acceptor
>  4700  OXT O.co2   acceptor
>  4701  ZNA    Zn   null
>Shouldn't Zinc have some information about this? I thought it was a donor.
>How do I incorporate this information into the tables. Is there any way I
>can do this?
>  4698    C   C.2 Carbon_sp/sp2        1 19
>  4699    O O.co2 Oxygen_Sp2           1 17
>  4700  OXT O.co2 Oxygen_Sp2           1 17
>  4701  ZNA    Zn null                 0 0
>Shouldn't Zinc have some type associated with it or some VDW parameters
>associated with it?
>Your help will be sincerely appreciated.
>Dock-fans mailing list
>Dock-fans at docking.org

P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986


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