Subject: W:How to parameters Mg+2 and Zn+2 in AUTODOCK?

From: "Xi, , Chen" <xchen7 /a\ uky.edu>
Date: Wed, 18 May 2005 01:09:05 -0400

Dear CCLers,
   In my study AUTODOCK3.05 tools was employed to dock a ligand containg CNOPH elments into a receptor containing Zn+2 and Mg+2 metal ions.  Zn+2 was bonded with amino residues of the recepter and Mg+2 was binded with amin residue, hydroxide ion and water mocules. I use the "mkgpf3" script to generate the gpf file. Before this step, the variable "PROTEIN_ATOMTYPES" in
file gpf3gen.awk was set with value "CNOSHZM". Then I use mkdpf3 to
generate dpf file without any other modification. Then I run AUTOGRID3
and AUTODOCK3. In the log file of  AUTOGRID3 output,  I found Zn was
set to atom type 8 without name and an error message --  "Devided by
zero was prevented. Was atom 3309 and 3320 the same?". However, I did
not find any atom situated too close in the receptor.  In the
AUTODOCK3 output, I found most of the resulted conformations have
large docking energies. Visualizing the docking results with adt, I
found in most docked conformation that one oxygen atom of the ligand
almost take the place of Mg+2 atom. I am puzzled with the problem. It seems that the problem is caused by parameters for Zn+2 and Mg+2 are not suitable in my study case. Could you give me a solution to fix these problems? Thanks you very much!
Sincerely
Xi   Chen
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Dr. Xi Chen
409 College of Pharmacy,907 Rose street
Lexingtong, KY 40536, USA
Tel: 859-323-4669
Email: xchen7 /a\ uky.edu
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