Re: Fwd: Re: AMBER: Pang-model of Zn2+

From: Oliver Hucke <>
Date: Fri, 26 Mar 2004 13:29:24 -0800

Dear Yuan-Ping, Kennie and Peter,

thanks a lot for your comments on my questions regarding the cationic
dummy atom approach to modeling Zn+2!

The first thing I was looking at after encountering the fusion problem
were indeed the van der Waals radii of the zinc and the hydroxyl-oxygen.
Both seemed to be o.k. as far as I can see from inspecting the atom
properties with xleap.

Applying the same minimization protocol with a h2o molecule replacing
the hydroxyl this problem did not occur.
It did also not occur with HO- when I increased the force constant for
the zinc dummy bond by a factor of 10.

I am still trying to find out what made the hydroxyl fuse with the
dummy. I will let you know in case I come to a conclusion.

Is anything speaking against a higher force constant for the zinc-dummy

Thanks agains,

Yuan-Ping Pang, Ph.D. wrote:
> Dear Oliver,
> Peter's email should solve your problem. The "fusion" problem should be
> ruled out if you correctly set the van der Waals parameters for the
> central zinc atom. Please let me know if there are problems that I am
> not aware of.
> My additional comment is that you don't have to use the positional
> constraints during minimization or heating. Occasionally, when working
> with protein structures with close contacts, you do have to first
> minimize the tetrahedral zinc system for a few steps (50 steps) with a
> positional constraint applied to the protein or first minimize the
> protein or the first-shell coordinates with a positional constraint
> applied to the tetrahedral zinc system to remove the close contacts, and
> then minimize the whole system without any constraint.
> Also I trust you have read the papers on the cationic dummy atom
> approach, especially Peter's paper in Protein Eng, and know that the
> cationic dummy atom approach is developed to solve the problems that
> Kennie described in his email to you this morning.
> Best regards,
> Yuan-Ping


Oliver Hucke, Dr.
                               Health Sciences Building - K418C
University of Washington 1959 NE Pacific St.
Dept. of Biochemistry phone: (206) 685 7046
Box 357742 fax : (206) 685 7002
Seattle, WA 98195-7742 email:

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Received on Fri Mar 26 2004 - 21:53:00 PST
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