[Dock-fans] DMS and Zn ion

Terry Lang terry at cgl.ucsf.edu
Mon Nov 14 17:27:35 PST 2005


Dear Sameer,

          See the previous email for the answer to your first question.  
For your second questions, get_near_res is now considered a legacy 
accessory.  You can download it from the same web site as DOCK 5, 
however it is no longer supported or maintained by the lab.  You should 
be able to select a small section of a protein using any visualization 
program.  There is a list of example programs on the DOCK web site at 
http://dock.compbio.ucsf.edu/DOCK_Links/index.htm. 

Sincerely,
Terry


kawatkar at chem.uga.edu wrote:

>Hi all,
>
>I sent an email about an hour ago about SPHGE failure while computing
>spheres for a protein binding site with Zn+2 ion in it. I tried without Zn
>and it apparantly worked (it gave me error about # of atoms being more
>than 15000, but atleast it did not give me previous error).
>
>1. I looked at the DMS created surface and it did not calulated surface
>for Zn ion. Do we have to mention anything specific about it? I checked
>the radii file for the VDW radii in dms and it mentions ZN. So DMS should
>recognise Zn+2 ion while computing the surface. Am I wrong? Can anybody
>address this problem.
>
>2. DOCK 4 manual metions a accesory called get_near_res to generate a file
>with specific atoms of protein to be used to create the surface. Does DOCK
>5 also has this program? I could not find it in the dock destribution that
>I have. I am using Dock 5.2.
>
>Thank you for your help,
>
>###################################################
>
>Sameer P. Kawatkar
>Complex Carbohydrate Research Center,
>University of Georgia,
>315 Riverbend Road,
>Athens, GA 30602.
>
>Phone: 706-542-0263
>URL: http://glycam.ccrc.uga.edu/users/sameer/index.html
>
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>Dock-fans mailing list
>Dock-fans at docking.org
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>  
>

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

 





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