[Dock-fans] DMS and Zn ion

Le Tien Dung letiendzung at yahoo.com
Sat Nov 12 00:44:42 PST 2005


hi
  did you try with Deep View ? I think you can use Deep View to select the sub portion of your protein and save the selected residues into a separate file.
   
  Cheers
   
  Le

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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