Subject: Zn+2 solvation parameters needed for Autodock

From: Susan Heffron <[email-masked]>
Date: Wed, 01 May 2002 17:45:11 -0700

Dear all,

I have recently started using Autodock 3.0, along with AutoDockTools. 
My protein is a metalloenzyme with zinc in the active site.  I've gotten
the 12-6 lj params for zinc from lj4.py, and have adjusted them with the
new 3.0 coefficients.  Is this correct?  What I still need, though, are
the solvation parameters for the pdbqs file.  Does anyone have, or know
where to get, the solvation parameters for Zn+2?

I also have a question about how to treat the ligands that I'm trying to
dock.  The ligand should have an ionized nitrogen (-1) that interacts
with the zinc.  How should this be modeled in the pdbq ligand file? 
Should this nitrogen be a different atom type than other nitrogens? 
Would the lj parameters be different?  I've tried removing one of the
two hydrogens and setting the charge on the nitrogen to -1.0, and this
comes close to putting the nitrogen in the "right" place relative to the
zn.  (With both hydrogens present, it is not docked correctly.) Is there
anything else that I should do?  I'm hoping that the missing zn
solvation parameters in the macromolecule pdbqs file are the problem,
and that if they are included (instead of being left as 0 0), that that
will solve the problem.  Any suggestion appreciated!

                          Thanks,
                          Susan
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        Susan Heffron
Dept. of Physiology and Biophysics                               
University of California, Irvine                
 Irvine, CA  92697-4560   U.S.A.                         
    phone:  (949) 824-4625
    FAX:    (949) 824-8540
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